Drug design for tubulin inhibitors, compositions, and methods of treatment thereof

ABSTRACT

The present invention relates to a computer-assisted method of a designing of a tubulin inhibitor comprising: a) determining an interaction between a tubulin protein and a chemical known to bind the tubulin protein by evaluating a binding of the tubulin protein to the chemical known to bind the tubulin protein; b) based on the interaction, designing a candidate tubulin inhibitor; c) determining an interaction between the tubulin protein and the candidate tubulin inhibitor by evaluating a binding of the tubulin protein to the candidate tubulin inhibitor; and d) concluding that the candidate tubulin inhibitor inhibits the tubulin protein wherein the conclusion is based on the interaction of step c). The invention also provides compositions and methods of treatment of diseases with the candidate tubulin inhibitors.

CROSS-REFERENCE

This application is a divisional application of U.S. patent applicationSer. No. 11/850,620, filed on Sep. 5, 2007, which claims priority toU.S. Provisional Patent Application No. 60/842,480, filed Sep. 5, 2006,all of which are incorporated herein by reference in their entirety.

BACKGROUND OF THE INVENTION

Tubulin proteins are essential building blocks of the microtubules ofcells, which in turn form a major part of the cellular cytoskeleton andare involved in important cellular functions including intracellulartransport, maintenance of cell shape, chromosome segregation duringmitosis, and cell motility. Polymers of alpha and beta tubulin subunitheterodimers form hollow cylindrical filament structures which comprisethe microtubules. The dynamic between microtubular polymerization anddepolymerization is essential to mitosis.

There exist multiple isoforms of the alpha and beta tubulin proteins,with distinct patterns of expression amongst different types of cellssuch as brain and hematopoietic cells (Drukman et al. 2002,International Journal of Oncology, 21:621-28.). Additionally, some formsof tubulin exist ubiquitously.

Because of the role microtubules play in mitosis, they are attractivetargets for chemotherapeutic intervention for cancer. Drugs affectingmicrotubule function have primarily targeted the alpha and beta tubulinheterodimers, and have been shown to have various binding sites on theheterodimer (Hadfield et al., 2003, Progress in Cell Cycle Research,5:309-25). Such sites include colchicine, vinca alkaloid, paclitaxel,and other binding sites.

Drugs targeting tubulin form two main families:microtubule-destabilizers and microtubule-stabilizers. Destabilizingagents include the vinca alkaloids, such as vincristine, vinblastine,and vinorelbine. Their mechanism of action is thought to be throughtubulin self-association, causing formation of structures other than thenormal hollow cylinders of normal microtubules. Stabilizing agentsinclude taxanes like paclitaxel and docetaxel. Their mechanism of actioncauses the microtubule to stabilize and prevents it from depolymerizing,disrupting the polymerization/depolymerization equilibrium essential formitosis.

Despite the existence of tubulin-targeting drugs, cancer cells also haveexhibited an ability to overcome their effects, becoming resistant tosuch chemotherapeutic agents. Examples of resistance mechanisms totubulin-targeting drugs include increased expression and activity of thedrug resistant P-glycoprotein (“P-gp”) pump, altered expression oftubulin subtypes and isoforms, mutations in tubulin proteins includingin drug binding sites, and post-translational modifications of tubulinproteins such as acetylation. These resistance mechanisms reveal thatthere is a need for novel chemotherapeutic agents that target tubulin,yet are less susceptible to chemotherapeutic drug resistance.

The identification of tubulin inhibitors can be attempted using methodssuch as screening of large numbers of random libraries of natural and/orsynthetic compounds. However, this method is inefficient in that ittypically results in a small number of positive “hits” and isconstrained by logistical factors accompanying large screeningprocesses.

Another method of such identification is structure-based drug design(“SBDD”). SBDD comprises a number of integrated components includingstructural information (eg. spectroscopic data like X-ray or magneticresonance information, relating to enzyme structure and/or conformation,protein-ligand interactions, etc.), computer modeling, medicinalchemistry, and biological testing (both in vivo and in vitro). Thesecomponents, each alone or in combination, are useful for acceleratingthe drug discovery process, for gaining insight into disease and diseaseprocesses, and for providing a more efficient method for identifyingdrug candidates.

Accordingly, the present invention provides compositions and methodsrelated to a design of candidate tubulin inhibitor s and methods oftreatment thereof.

SUMMARY OF THE INVENTION

One aspect of the present invention relates to a computer-assistedmethod of a designing of a tubulin inhibitor by a) determining aninteraction between a tubulin protein and a chemical known to bind thetubulin protein by evaluating a binding of the tubulin protein to thechemical known to bind the tubulin protein; b) based on the interaction,designing a candidate tubulin inhibitor; c) determining an interactionbetween the tubulin protein and the candidate tubulin inhibitor byevaluating a binding of the tubulin protein to the candidate tubulininhibitor; and d) ascertaining that the candidate tubulin inhibitorinhibits the tubulin protein wherein the conclusion is based on theinteraction of step c). In some embodiments, the tubulin protein is athree-dimensional structure comprising a binding domain of the tubulinprotein. In some embodiments, the binding domain of the tubulin proteinis for example, colchicine binding domain, vinblastine binding domain,and paclitaxel binding domain. In some embodiments, the tubulin proteinis derived from a crystal of the tubulin protein. In some embodiments,the designing is performed in conjunction with a computer modeling. Insome embodiments, the binding domain of the tubulin protein is anintradimer surface. In some other embodiments, the binding domain of thetubulin protein is an interdimer surface. In still some embodiments, thebinding domain of the tubulin protein is a surface facing inside of amicrotubule near an interprotofilament interface at a distance from anylongitudinal interface. In some embodiments, the surface is a paclitaxelbinding site.

In some embodiments of the aforementioned aspect of the presentinvention, the designing involves replacing a substituent on thechemical known to bind the tubulin protein with another substituentwherein the other substituent improves the binding of the candidatetubulin inhibitor with the tubulin protein. In some embodiments, theinteraction is for example, steric interaction, van der Waalsinteraction, electrostatic interaction, solvation interaction, chargeinteraction, covalent bonding interaction, non-covalent bondinginteraction, entropically favorable interaction, enthalpically favorableinteraction, or a combination thereof. In some embodiments, thecandidate tubulin inhibitor is an analogue of the chemical known to bindthe tubulin protein. In some embodiments, the chemical known to bind thetubulin protein is a ketone that is a thyroxine analogue. In still someembodiments, the method further comprises of a step of chemicallysynthesizing the candidate tubulin inhibitor. In some embodiments, themethod further comprises of evaluating a tubulin inhibitory activity ofthe candidate tubulin inhibitor and selecting the candidate tubulininhibitor based on the evaluation. In some embodiments, the evaluationof the tubulin inhibiting activity involves an assay technique.

In some embodiments of the aforementioned computer-assisted method of adesigning of a tubulin inhibitor, the candidate tubulin inhibitor is acompound of formula I, its pharmaceutically acceptable salts, orprodrugs thereof:

wherein: R₁ and R₅ are halogens; R₂, R₃, and R₄ are independentlyselected from the group consisting of hydrogen, hydroxyl, halogen,ester, optionally substituted alkoxy, optionally substituted amine,phosphate, optionally substituted alkyl, and optionally substitutedacetyl; and R₆, R₇, R₈, R₉, and R₁₀ are independently selected from thegroup consisting of hydrogen, hydroxyl, halogen, optionally substitutedalkoxy, optionally substituted amine, phosphate, optionally substitutedalkyl, optionally substituted alkenyl, optionally substituted alkynyl,nitroso, carboxyl, optionally substituted cycloalkyl, and optionallysubstituted heterocyclic.

In some embodiments of the aforementioned aspect, the candidate tubulininhibitor is a compound of formula II or its pharmaceutically acceptablesalts or prodrugs:

wherein: R, R′, R₂, R₄, R₆, R₇, R₉, and R₁₀ are independently selectedfrom the group consisting of hydrogen, hydroxyl, halogen, optionallysubstituted alkoxy, optionally substituted amine, phosphate, optionallysubstituted alkyl, and optionally substituted acetyl.

In some embodiments, the candidate tubulin inhibitor is a compound offormula III or its pharmaceutically acceptable salts or prodrugs:

wherein: R₆, R₇, R₉, and R₁₀ are independently selected from the groupconsisting of hydrogen, hydroxyl, optionally substituted amine,phosphate, and optionally substituted alkyl.

In some embodiments, the candidate tubulin inhibitor is1-(4-(3-hydroxy-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone, representedby formula IIIA or its pharmaceutically acceptable salts or prodrugs:

In some embodiments, the candidate tubulin inhibitor is1-(4-(3-amino-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone, representedby formula IIIB or its pharmaceutically acceptable salts or prodrugs:

In some embodiments, the candidate tubulin inhibitor is a compound offormula IIIC or its pharmaceutically acceptable salts or prodrugs:

In some embodiments, the candidate tubulin inhibitor is mono(5-methoxy-3-(4-acetyl-2,6-iodophenoxy)phenyl) phosphoric acid ester,represented by formula IIID or its pharmaceutically acceptable salts orprodrugs:

In some embodiments, the optionally substituted alkyl is substitutedwith an optionally substituted heterocyclic. In some embodiments, theoptionally substituted heterocyclic is for example, azeridine,azetidine, pyrrole, dihydropyrrole, pyrrolidene, pyrazole, pyrazoline,pyrazolidine, imidazole, benzimidazole, triazole, tetrazole, oxazole,isoxazole, benzoxazole, oxadiazole, oxazoline, oxazolidine, thiazole,isothiazole, pyridine, dihydropyridine, tetrahydropyridine, quinazoline,pyrazine, pyrimidine, pyridazine, quinoline, isoquinoline, triazine,tetrazine, and piperazine.

In some embodiments, the candidate tubulin inhibitor is the compound1-(4-(2-(N-piperazinylprop-3-yl))-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone,represented by formula IIIE or its pharmaceutically acceptable salts orprodrugs:

Another aspect of the invention relates to a computer system containinga set of information to perform a design of a tubulin inhibitor having auser interface comprising a display unit, the set of informationcomprises a) logic for inputting an information regarding a binding of atubulin protein to a chemical known to bind tubulin protein; b) logicfor designing a candidate tubulin inhibitor based on the binding of thetubulin protein to the chemical known to bind tubulin protein; c) logicfor determining an information regarding a binding of the tubulinprotein to the candidate tubulin inhibitor; and d) logic for making aconclusion regarding a tubulin inhibitory properties of the candidatetubulin inhibitor based on the determination of step c).

Yet another aspect of the invention relates to a computer-readablestorage medium containing a set of information for a general purposecomputer having a user interface comprising a display unit, the set ofinformation comprises a) logic for inputting an information regarding abinding of a tubulin protein to a chemical known to bind tubulinprotein; b) logic for designing a candidate tubulin inhibitor based onthe binding of the tubulin protein to the chemical known to bind tubulinprotein; c) logic for determining an information regarding a binding ofthe tubulin protein to the candidate tubulin inhibitor; and d) logic formaking a conclusion regarding a tubulin inhibitory properties of thecandidate tubulin inhibitor based on the determination of step c). Insome embodiments, the chemical is a ketone which is a thyroxineanalogue. In some embodiments, the chemical is a ketone which is athyroxine analogue.

Yet another aspect of the invention relates to an electronic signal orcarrier wave that is propagated over the internet between computerscomprising a set of information for a general purpose computer having auser interface comprising a display unit, the set of informationcomprising a computer-readable storage medium containing a set ofinformation for a general purpose computer having a user interfacecomprising a display unit, the set of information comprises a) logic forinputting an information regarding a binding of a tubulin protein to achemical known to bind tubulin protein; b) logic for designing acandidate tubulin inhibitor based on the binding of the tubulin proteinto the chemical known to bind tubulin protein; c) logic for determiningan information regarding a binding of the tubulin protein to thecandidate tubulin inhibitor; and d) logic for making a conclusionregarding a tubulin inhibitory properties of the candidate tubulininhibitor based on the determination of step c).

Another aspect of the invention relates to a method of treating adisease by administering to a patient in need thereof an effectiveamount of at least one compound of formula I, its pharmaceuticallyacceptable salts, or prodrugs thereof:

wherein: R₁ and R₅ are halogens; R₂, R₃, and R₄ are independentlyselected from the group consisting of hydrogen, hydroxyl, halogen,ester, optionally substituted alkoxy, optionally substituted amine,phosphate, optionally substituted alkyl, and optionally substitutedacetyl; and R₆, R₇, R₈, R₉, and R₁₀ are independently selected from thegroup consisting of hydrogen, hydroxyl, halogen, optionally substitutedalkoxy, optionally substituted amine, phosphate, optionally substitutedalkyl, optionally substituted alkenyl, optionally substituted alkynyl,nitroso, carboxyl, optionally substituted cycloalkyl, and optionallysubstituted heterocyclic.

In some embodiments of aforementioned method of treating a disease, thecompound is of formula II or its pharmaceutically acceptable salts orprodrugs:

wherein: R, R′, R₂, R₄, R₆, R₇, R₉, and R₁₀ are independently selectedfrom the group consisting of hydrogen, hydroxyl, halogen, optionallysubstituted alkoxy, optionally substituted amine, phosphate, optionallysubstituted alkyl, and optionally substituted acetyl. In someembodiments, the compound is of formula III or its pharmaceuticallyacceptable salts or prodrugs:

wherein: R₆, R₇, R₉, and R₁₀ are independently selected from the groupconsisting of hydrogen, hydroxyl, optionally substituted amine,phosphate, and optionally substituted alkyl. In some embodiments, thecompound is 1-(4-(3-hydroxy-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone,represented by formula IIIA or its pharmaceutically acceptable salts orprodrugs:

In some embodiments, the compound is1-(4-(3-amino-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone, representedby formula IIIB or its pharmaceutically acceptable salts or prodrugs:

In some embodiments, the compound is1-(4-(2-amino-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone, representedby formula IIIC or its pharmaceutically acceptable salts or prodrugs:

In some embodiments, the compound is mono(5-methoxy-3-(4-acetyl-2,6-iodophenoxy)phenyl) phosphoric acid ester,represented by formula IIID or its pharmaceutically acceptable salts orprodrugs:

In some embodiments, the optionally substituted alkyl is substitutedwith an optionally substituted heterocyclic. In some embodiments, theoptionally substituted heterocyclic is for example, azeridine,azetidine, pyrrole, dihydropyrrole, pyrrolidene, pyrazole, pyrazoline,pyrazolidine, imidazole, benzimidazole, triazole, tetrazole, oxazole,isoxazole, benzoxazole, oxadiazole, oxazoline, oxazolidine, thiazole,isothiazole, pyridine, dihydropyridine, tetrahydropyridine, quinazoline,pyrazine, pyrimidine, pyridazine, quinoline, isoquinoline, triazine,tetrazine, and piperazine. In some embodiments, the candidate tubulininhibitor is1-(4-(2-(N-piperazinylprop-3-yl))-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone,represented by formula IIIE or its pharmaceutically acceptable salts orprodrugs:

In some embodiments, the treating comprises inhibiting tubulin proteinfunction. In some embodiments, the disease is for example, cancer,inflammation, metabolic disease, gout, CVS disease, CNS disease,disorder of the hematolymphoid system, disorder of endocrine andneuroendocrine, disorder of urinary tract, disorder of respiratorysystem, disorder of female genital system, and disorder of male genitalsystem.

Another aspect of the present invention relates to a compound of formulaI or its pharmaceutically acceptable salts or prodrugs:

wherein: R₁ and R₅ are halogens; R₂, R₃, and R₄ are independentlyselected from the group consisting of hydrogen, hydroxyl, halogen,ester, optionally substituted alkoxy, optionally substituted amine,phosphate, optionally substituted alkyl, and optionally substitutedacetyl; and R₆, R₇, R₈, R₉, and R₁₀ are independently selected from thegroup consisting of hydrogen, hydroxyl, halogen, optionally substitutedalkoxy, optionally substituted amine, phosphate, optionally substitutedalkyl, optionally substituted alkenyl, optionally substituted alkynyl,nitroso, carboxyl, optionally substituted cycloalkyl, and optionallysubstituted heterocyclic. Preferably, the compound is a tubulininhibitor.

In some embodiments, the compound is of formula II or itspharmaceutically acceptable salts or prodrugs:

wherein: R, R′, R₂, R₄, R₇, R₉, and R₁₀ are independently selected fromthe group consisting of hydrogen, hydroxyl, halogen, optionallysubstituted alkoxy, optionally substituted amine, phosphate, optionallysubstituted alkyl, and optionally substituted acetyl. Preferably, thecompound is a tubulin inhibitor.

In some embodiments, the compound is of formula III or itspharmaceutically acceptable salts or prodrugs:

-   -   wherein: R₆, R₇, R₉, and R₁₀ are independently selected from the        group consisting of hydrogen, hydroxyl, optionally substituted        amine, phosphate, and optionally substituted alkyl Preferably,        the compound is a tubulin inhibitor.

In some embodiments, the compound is1-(4-(3-hydroxy-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone, representedby formula IIIA or its pharmaceutically acceptable salts or prodrugs:

In some embodiments, the compound is1-(4-(3-amino-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone1-(4-(3-amino-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone, representedby formula IIIB or its pharmaceutically acceptable salts or prodrugs:

In some embodiments, the compound is1-(4-(2-amino-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone, representedby formula IIIC or its pharmaceutically acceptable salts or prodrugs:

In some embodiments, the compound is mono(5-methoxy-3-(4-acetyl-2,6-iodophenoxy)phenyl) phosphoric acid ester,represented by formula IIID or its pharmaceutically acceptable salts orprodrugs:

In some embodiments of the aforementioned aspect of the invention, theoptionally substituted alkyl is substituted with an optionallysubstituted heterocyclic. In some embodiments, the optionallysubstituted heterocyclic is for example, azeridine, azetidine, pyrrole,dihydropyrrole, pyrrolidene, pyrazole, pyrazoline, pyrazolidine,imidazole, benzimidazole, triazole, tetrazole, oxazole, isoxazole,benzoxazole, oxadiazole, oxazoline, oxazolidine, thiazole, isothiazole,pyridine, dihydropyridine, tetrahydropyridine, quinazoline, pyrazine,pyrimidine, pyridazine, quinoline, isoquinoline, triazine, tetrazine,and piperazine. In some embodiments, the compound is1-(4-(2-(N-piperazinylprop-3-yl))-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone,represented by formula IIIE or its pharmaceutically acceptable salts orprodrugs:

Some embodiments of the aforementioned aspect of the present inventionrelate to a pharmaceutical composition comprising an effective amount ofat least one compound of the present invention and a pharmaceuticallyacceptable carrier.

Some embodiments provide a process of manufacturing a compound offormula IIIB or its pharmaceutically acceptable salts or prodrugs:

The process comprises: (a) nitrating1-(3,5-diiodo-4-(4-methoxyphenoxy)phenyl)ethanone to form as anintermediate 1-(3,5-diiodo-4-(4-methoxy-3-nitrophenoxy)phenyl)ethanone;and (b) reducing the intermediate of step (a) to form the compound offormula IIIB. In some embodiments, the nitrating is carried out in thepresence of nitric acid and concentrated sulfuric acid in an organicsolvent. In some embodiments, the organic solvent is methylene chloride.In some embodiments, the reducing is carried out in the presence oftin(II) chloride.

Some embodiments of the invention provide a process of manufacturing acompound of formula IIIA or its pharmaceutically acceptable salts orprodrugs:

The process comprises: (a) reacting a compound of formula IIIB or itspharmaceutically acceptable salts or prodrugs:

with a metal nitrate in the presence of a strong acid to form adiazonium intermediate; and (b) refluxing the diazonium intermediate inthe presence of a strong acid to form the compound of formula IIIA. Insome embodiments, the metal nitrate is sodium nitrate. In someembodiments, the strong acid of step (a) is sulfuric acid. In someembodiments, the strong acid of step (b) is sulfuric acid. In someembodiments, the strong acid of step (a) and step (b) is sulfuric acid.Other aspects, characteristics and advantages will become clear uponconsideration of the instant disclosure, including the appended drawingsand original claims.

INCORPORATION BY REFERENCE

All publications and patent applications mentioned in this specificationare herein incorporated by reference to the same extent as if eachindividual publication or patent application was specifically andindividually indicated to be incorporated by reference.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the invention are set forth with particularity inthe appended claims. A better understanding of the features andadvantages of the present invention will be obtained by reference to thefollowing detailed description that sets forth illustrative embodiments,in which the principles of the invention are utilized, and theaccompanying drawings of which:

FIG. 1 is a flow chart showing the steps of the methods as disclosedherein.

FIG. 2 illustrates a computer for implementing selected operationsassociated with the methods disclosed herein.

FIG. 3 illustrates a tubulin X-ray structural data analysis.

FIG. 4A illustrates a binding pose of methyl3,5-diiodo-4-(4′-methoxyphenoxy)-benzoate (as thick sticks) in tubulin.A bound conformation of colchicine from experimentally determinedstructure is superimposed (thin sticks).

FIG. 4B depicts the methyl 3,5-diiodo-4-(4′-methoxyphenoxy)-benzoate asthick sticks and colchicine as thin sticks.

FIG. 5 illustrates a binding of the tubulin inhibitor with at least tworesidues that differ between isotypes.

FIG. 6 illustrates the cell-cycle arrest caused by1-(3,5-diiodo-4-(3-amino-4-methoxyphenoxy)phenylethanone, a PARP-1inhibitor disclosed herein as Formula IIIB(1-(4-(3-amino-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone), as comparedto control, methyl 3,5-diiodo-4-(4-methoxyphenyloxy)benzyl ketone(1-[3,5-diiodo-4-(4′-methoxyphenoxy)-phenyl]-ethanone (DIPE)).

FIG. 7 illustrates the induction of apoptosis in HeLa cells induced bythe compound of Formula IIIB(1-(4-(3-amino-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone), as comparedto control, methyl 3,5-diiodo-4-(4-methoxyphenyloxy)benzyl ketone(1-[3,5-diiodo-4-(4′-methoxyphenoxy)-phenyl]-ethanone (DIPE)).

DETAILED DESCRIPTION OF THE INVENTION Definitions

The term, “aryl” refers to optionally substituted mono- or bicyclicaromatic rings containing only carbon atoms. The term can also includephenyl group fused to a monocyclic cycloalkyl or monocycliccycloheteroalkyl group in which the point of attachment is on anaromatic portion. Examples of aryl groups include, e.g., phenyl,naphthyl, indanyl, indenyl, tetrahydronaphthyl, 2,3-dihydrobenzofuranyl,dihydrobenzopyranyl, 1,4-benzodioxanyl, and the like.

The term, “heterocyclic” refers to an optionally substituted mono- orbicyclic aromatic ring containing at least one heteroatom (an atom otherthan carbon), such as N, O and S, with each ring containing about 5 toabout 6 atoms. Examples of heterocyclic groups include, e.g., pyrrolyl,isoxazolyl, isothiazolyl, pyrazolyl, pyridyl, oxazolyl, oxadiazolyl,thiadiazolyl, thiazolyl, imidazolyl, triazolyl, tetrazolyl, furanyl,triazinyl, thienyl, pyrimidyl, pyridazinyl, pyrazinyl, benzoxazolyl,benzothiazolyl, benzimidazolyl, benzofuranyl, benzothiophenyl,furo(2,3-b)pyridyl, quinolyl, indolyl, isoquinolyl, and the like.

The term, “computer system” as used herein, means the hardware means,software means and data storage means used to perform method of thepresent invention. Preferably, the computer system is used to analyzeatomic coordinate data. The minimum hardware means of the computer-basedsystems of the present invention comprises a central processing unit(CPU), input means, output means and data storage means. Desirably amonitor is provided to visualize the structure data. The computer can bea stand-alone, or connected to a network and/or shared server. The datastorage means can be RAM or means for accessing computer readable mediaof the invention.

The term, “computer readable media” as used herein, means any mediawhich can be read and accessed by a computer, for example, the media issuitable for use in the above-mentioned computer system. The mediainclude, but are not limited to: magnetic storage media such as floppydiscs, hard disc storage medium and magnetic tape; optical storage mediasuch as optical discs or CD-ROM; electrical storage media such as RAMand ROM; and hybrids of these categories such as magnetic/opticalstorage media.

The term “inhibit” or its grammatical equivalent, such as “inhibitory,”is not intended to require complete reduction in biological activity,preferably, tubulin activity. Such reduction is preferably by at leastabout 50%, at least about 75%, at least about 90%, and more preferablyby at least about 95% of the activity of the molecule in the absence ofthe inhibitory effect, e.g., in the absence of a tubulin inhibitor asdisclosed in the invention. Most preferably, the term refers to anobservable or measurable reduction in activity. In treatment scenarios,preferably the inhibition is sufficient to produce a therapeutic and/orprophylactic benefit in the condition being treated.

The term “model” or its grammatical equivalents, such as, “modeling” asused herein, means the quantitative and qualitative analysis ofmolecular structure and/or function based on atomic structuralinformation and interaction models. The term “modeling” includes forexample, conventional numeric-based molecular dynamic and energyminimization models, interactive computer graphic models, modifiedmolecular mechanics models, distance geometry and other structure-basedconstraint models.

The term “pharmaceutically acceptable salt” as used herein, means thosesalts which retain the biological effectiveness and properties of thecompounds of the present invention, and which are not biologically orotherwise undesirable.

The term “substituted” includes single or multiple degrees ofsubstitution by a named substituent.

The term “candidate tubulin inhibitor” as used herein, means anycompound which is potentially capable of associating with any of thealpha, beta, or gamma tubulin proteins, and/or inhibiting tubulinprotein activity and/or the ability of tubulin protein to interact withanother molecule or to form microtubule polymers. The candidate compoundmay be designed or obtained from a library of compounds which maycomprise peptides, as well as other compounds, such as small organicmolecules and particularly new lead compounds. By way of example, thecandidate compound may be a natural substance, a biologicalmacromolecule, or an extract made from biological materials such asbacteria, fingi, or animal (particularly mammalian) cells or tissues, anorganic or an inorganic molecule, a synthetic test compound, asemi-synthetic test compound, a carbohydrate, a monosaccharide, anoligosaccharide or polysaccharide, a glycolipid, a glycopeptide, asaponin, a heterocyclic compound, a structural or functional mimetic, apeptide, a peptidomimetic, a derivatized test compound, a peptidecleaved from a whole protein, or a peptides synthesized synthetically(such as, by way of example, either using a peptide synthesizer or byrecombinant techniques or combinations thereof), a recombinant testcompound, a natural or a non-natural test compound, a fusion protein orequivalent thereof and mutants, derivatives or combinations thereof.

The term “treating” or its grammatical equivalents as used herein, meansachieving a therapeutic benefit and/or a prophylactic benefit. Bytherapeutic benefit is meant eradication or amelioration of theunderlying disorder being treated. Also, a therapeutic benefit isachieved with the eradication or amelioration of one or more of thephysiological symptoms associated with the underlying disorder such thatan improvement is observed in the patient, notwithstanding that thepatient may still be afflicted with the underlying disorder. Forprophylactic benefit, the compositions may be administered to a patientat risk of developing a particular disease, or to a patient reportingone or more of the physiological symptoms of a disease, even though adiagnosis of this disease may not have been made.

The term “anti-vascular” refers to an agent or method that reduces theamount of blood vessels supplying a tumor that exist before orimmediately before the administration of the agent or the implementationof the method.

The term “tubulin heterodimer” refers to an alpha tubulin protein andbeta tubulin protein subunit complex, comprising the building blocs formicrotubule polymerization.

The term “thyroid hormone analogue” or “thyroid hormone/analogue”include both naturally-occurring thyroid hormones such as thyroxine, andchemicals similar in structure to the naturally-occurring thyroidhormones. The chemicals that are similar in structure to thenaturally-occurring thyroid hormones may have similar or differentbiological and pharmacological properties as compared to thenaturally-occurring thyroid hormones.

The term “tubulin protein” includes single tubulin gene products,variants, or splice variants thereof, and also includes tubulin proteinheterodimers such as, but not limited to, heterodimers of the alpha andbeta tubulin protein gene products.

The term “tubulin inhibitor” includes any agent that inhibits thebiological activity of a tubulin protein, and includes analogues ofthyroxine.

Methods for a Design of a Tubulin Inhibitor

One aspect of the present invention relates to methods for design of atubulin inhibitor. In some preferred embodiments, the designingcomprises using computer modeling techniques. In particular, the presentinvention relates to a computer-assisted method of a design of a tubulininhibitor comprising: a) determining an interaction between a tubulinprotein and a chemical known to bind the tubulin protein by evaluating abinding of the tubulin protein to the chemical known to bind the tubulinprotein; b) based on the interaction, designing a candidate tubulininhibitor; c) determining an interaction between the tubulin protein andthe candidate tubulin inhibitor by evaluating a binding of the tubulinprotein to the candidate tubulin inhibitor; and d) concluding that thecandidate tubulin inhibitor inhibits the tubulin protein wherein theconclusion is based on the interaction of step c).

In some preferred embodiments, a three-dimensional structure comprisinga tubulin protein and a three-dimensional structure of the chemical isused for determining an interaction between the tubulin protein and thechemical. In some preferred embodiments, a three dimensional structureof a binding domain of a tubulin protein is modeled using a crystal ofalpha and beta tubulin protein heterodimers through x-raycrystallographic techniques. Preferably, the tubulin protein is thealpha-tubulin/beta tubulin heterodimer. A three dimensional structure ofa known tubulin inhibitor or thyroid hormone analogue is modeled basedon techniques known in the art. The three dimensional structure of aknown tubulin inhibitor or thyroid hormone is allowed to interact withthe three dimensional structure of a binding domain of the tubulinprotein. Various tubulin inhibitors and thyroid hormone analogues areknown in the art and are within the scope of the present invention. Someof the examples of the known tubulin inhibitors and thyroid hormoneanalogues include, but are not limited to, vinblastine, vincristine,vinorelbine, paclitaxel, docetaxel, colchicine, and thyroxine. In somepreferred embodiments of the present invention, the known tubulininhibitor is colchicine. In another preferred embodiment of the presentinvention, the thyroid hormone analogue is thyroxine.

An interaction between the tubulin protein or tubulin proteinheterodimer and the known tubulin inhibitor or thyroid hormone analogueis determined based on an evaluation of a three dimensional structure ofdomains of a tubulin protein bound to the known tubulin inhibitor orthyroid hormone analogue. The evaluation can comprise evaluation of oneor more of steric interactions, van der Waals interactions,electrostatic interactions, solvation interactions, charge interactions,covalent bonding interactions, non-covalent bonding interactions,entropically favorable interactions, enthalpically favorableinteractions, or a combination thereof. The techniques for theevaluation of the interaction between the protein and the drug are wellknown in the art and are well within the scope of the present invention.

FIG. 3 illustrates a tubulin X-ray structural data analysis.Small-molecule inhibitor binding pocket in tubulin is shown (greenblob). A colchicine molecule bound to the tubulin is shown in stickrepresentation. Surrounding amino-acid residues are labeled, dark bluefor beta-tubulin and magenta for alpha-tubulin.

Based on the evaluation of the binding of a known tubulin inhibitor withthe tubulin protein, a candidate tubulin inhibitor can be designed.Preferably, the candidate tubulin inhibitor is designed using computermodeling. In some preferred embodiments, the candidate tubulin inhibitoris an analogue of the known tubulin inhibitor. In still furtherpreferred embodiments, the candidate tubulin inhibitor is an analogue ofthe colchicine. In still further preferred embodiments, the candidatetubulin inhibitor is an analogue of the thyroid hormone thyroxine. Acandidate tubulin inhibitor can be designed in such a way that it fitsequally or more efficiently in the binding domain of the tubulin proteinas compared to the known tubulin inhibitor or thyroid-hormone analogue.

FIG. 4A illustrates a binding pose of methyl3,5-diiodo-4-(4′-methoxyphenoxy)-benzoate (as thick sticks) in tubulin.A bound conformation of colchicine from experimentally determinedstructure is superimposed (thin sticks). FIG. 4B depicts the methyl3,5-diiodo-4-(4′-methoxyphenoxy)-benzoate as thick sticks and colchicineas thin sticks. The compound structures are converted to 3D and dockedinto tubulin binding pocket using Molsoft's ICM-Dock.

FIG. 5 illustrates at least two residues that differ between isotypes(in particular isotype III). The two isotypes are in contact with theinhibitors. Differential affinity of tubulin inhibitors to isotypes maybe important for efficacy. For example, isotype 3 may be at leastpartially responsible for taxol resistance.

After the designing of the candidate tubulin inhibitor, an interactionbetween the tubulin protein or tubulin protein heterodimer and thecandidate tubulin inhibitor can be determined based on an evaluation ofthe three dimensional structure of the domains of the tubulin protein ortubulin protein heterodimer bound to the candidate tubulin inhibitor.The evaluation can comprise evaluation of one or more of stericinteractions, van der Waals interactions, electrostatic interactions,solvation interactions, charge interactions, covalent bondinginteractions, non-covalent bonding interactions, entropically favorableinteractions, enthalpically favorable interactions, or a combinationthereof. Based on the evaluation a conclusion can be made regarding thecandidate tubulin inhibitor that inhibits tubulin protein function.

Alternatively, the tubulin protein or tubulin heterodimer complex can beco-crystallized with a candidate tubulin inhibitor in order to provide acrystal suitable for determining the structure of the complex. A crystalof the tubulin protein or tubulin heterodimer complex can be soaked in asolution containing the candidate tubulin inhibitor in order to formco-crystals by diffusion of the candidate tubulin inhibitor into thecrystal of the tubulin protein. In some embodiments, the structure ofthe tubulin protein or tubulin heterodimer complex obtained in thepresence and absence of the candidate tubulin inhibitor can be comparedto determine structural information about the tubulin protein,identification of possible binding regions of the tubulin protein and/ordetermine the interaction between the candidate tubulin inhibitor andthe tubulin protein or tubulin heterodimer complex.

The present invention further relates to methods for synthesizing thecandidate tubulin inhibitors by conventional synthetic chemistrytechniques. These techniques are known in the art and are within thescope of the present invention. The present invention further relates toassessing the bioactivity, such as tubulin inhibiting activity, of thesynthesized tubulin inhibitor compounds. The assay techniques forassessing the bioactivity of the candidate tubulin inhibitor are wellknown in the art and are within the scope of the present invention.Another aspect of the present invention relates to providing methods oftreatment of a disease using the tubulin inhibitors. Preferably, thedisease is a condition that is related to tubulin function.

The steps to some of the preferable methods of the present invention aredepicted in FIG. 1. Without limiting the scope of the present invention,the steps can be performed independent of each other or one after theother. One or more steps can be skipped in the methods of the presentinvention. A tubulin protein or tubulin heterodimer is provided at step101. The tubulin protein or tubulin heterodimer may be provided as athree dimensional structure of a binding domain of a tubulin protein ortubulin heterodimer. The three dimensional structure of the tubulinprotein or tubulin heterodimer may be modeled from a crystal of tubulinprotein or tubulin protein heterodimer using x-ray crystallography. Achemical known to bind the tubulin protein or tubulin heterodimer isprovided at step 102. A three dimensional structure of the chemical maybe provided. The three dimensional structure of the chemical known tobind the tubulin protein or tubulin heterodimer may be provided by acomputer modeling technique. An interaction between the tubulin proteinor tubulin heterodimer and the chemical known to bind the tubulinprotein or tubulin heterodimer can be determined based on the evaluationof the three dimensional structure of the binding domain of the tubulinprotein or tubulin protein heterodimer bound to the chemical known tobind the tubulin protein or tubulin heterodimer at step 103. Based onthe evaluation, a candidate tubulin inhibitor can be designed at step104. The candidate tubulin inhibitor can be designed by computermodeling. An interaction between the tubulin protein or tubulinheterodimer and the candidate tubulin inhibitor can be determined basedon the evaluation of the three dimensional structure of the bindingdomain of the tubulin protein or tubulin protein heterodimer bound tothe candidate tubulin inhibitor at step 105. Based on this evaluation, aconclusion can be made regarding a candidate tubulin inhibitor thatinhibits tubulin protein function at step 106. Further, the candidatetubulin inhibitor that inhibits tubulin protein can be chemicallysynthesized at step 107. The chemically synthesized candidate tubulininhibitor can be assayed for its bioactivity, preferably, activity ininhibiting tubulin function at step 108. The candidate tubulin inhibitorthat inhibits tubulin protein or tubulin protein heterodimer can be usedfor treating diseases at step 109. It shall be understood that theinvention includes other methods not explicitly set forth herein.

Tubulin and Microtubules

Tubulin is a protein that comprises cellular microtubules. Two distincttubulin proteins, the alpha and beta protein subunits form heterodimersthat form polymers that in turn form the hollow cylinders that make upthe microtubular structure. Both the alpha and beta protein subunitsbind guanosine triphosphate (“GTP”), but only the beta protein subunithydrolyzes GTP to guanosine diphosphate (“GDP”). The molecular weight ofthe alpha and beta protein subunits is approximately 55 kilodaltons(“kDa”) each.

Microtubules are comprised of polymers of alpha/beta tubulinheterodimers, and form one of the components of the cell's cytoskeleton.They have a hollow cylindrical shape and their functions include, butare not limited to, cell motility, maintenance of cell shape,intracellular transport, and chromosomal segregation during mitosis.Microtubules grow through polymerization and nucleate in a microtubuleorganizing center. In these centers, an additional type of tubulinprotein, the gamma-tubulin, interacts with several other proteins andforms a ring structure called the “gamma-tubulin ring complex,” whichhelps to provide scaffolding for polymerization.

During polymerization, the microtubule grows by adding more alpha/betaheterodimers onto the “cap” or end of the microtubule. The cap of themicrotubule contains at least one alpha/beta heterodimer bound to GTP.Because GDP-bound alpha/beta heterodimers at the cap tend todepolymerize from the microtubule, the GTP-bound cap provides protectionagainst depolymerization, even though alpha/beta lower down the polymerare GDP-bound. Eventually, the GTP in the cap is hydrolyzed, creatingdepolymerization of the microtubule and accounting for the equilibriumbetween microtubule formation and depolymerization in cells.

Binding Domains of Tubulin

There are three drug families that target tubulin's function, andtherefore at least three binding sites have been described (for areview, see Downing et al., 1999, Cell Structure and Function,24:269-71). These include, but are not limited to, the colchicinebinding site, the vinca alkaloid binding site, and the paclitaxelbinding site. At least two binding sites have been characterized assites that induce destabilization of microtubular polymers: thecolchicine and vinca alkaloid binding sites. The paclitaxel binding sitehas been connected to increased microtubular polymer stability, and bothstability and depolymerization have been shown to cause cell death.

The colchicine binding site is approximately in the dimer's middle, nearthe interface of the alpha and beta tubulin proteins. It also appears tobe on the side of the heterodimer that faces the microtubular luminalsurface. The vinca alkaloid binding site is located near thelongitudinal inter-dimer surface, and is near the GTP/GDP nucleotidebinding site. The paclitaxel binding site is on the beta protein subunitof the dimer, and appears to be involved in dimer interfacing with otherpolymer strand dimers. Therefore, it is thought to be involved withpolymer strand lateral interaction, possibly strengthening it, since ithas a polymerization-stabilizing function.

Crystal Structure of Tubulin

Alpha and beta heterodimers of tubulin comprise the structural subunitof microtubules, and this subunit's crystal structure has been reported,with crystals induced using zinc (see Nogales et al., 1998, Nature,391:199-202). One embodiment of the invention utilizes the techniquesdescribed therein to crystallize tubulin protein or tubulin heterodimerswith which to determine the atomic coordinates. In one embodiment of theinvention, the structures of alpha and beta tubulin proteins are verysimilar as each protein has a core of two beta-sheets surrounded byalpha-helices. In another embodiment, each monomer has at least threefunctional domains including, but not limited to, the amino-terminaldomain (which contains the GTP/GDP nucleotide binding region, the vincaalkaloid binding-domains, and the colchicine binding domain), theintermediate domain (which contains the paclitaxel-binding domain), andthe carboxy-terminal domain (which is thought to contain the bindingregions for motor proteins).

Examples of methods for determining structure information of tubulinprotein, tubulin protein heterodimer, or either bound with a inhibitorinclude: 1) mass spectrometry to determine one or more properties of aprotein, including primary sequence, post translation modification,protein-small molecule interaction, or protein-protein interactionability; 2) NMR, including ID NMR, multidimensional NMR, andmultinuclear NMR, such as ¹⁵N/¹H HSQC spectra, to determine one or moreproperties of a protein including three dimensional structure,conformational states, aggregation level, state of protein folding orunfolding, or the dynamic properties of the protein; and 3) x-raycrystallography to determine one or more properties of a protein,including three dimensional structure, diffraction of its crystal formor its space group. The present invention preferably uses x-raycrystallography to determine the structural characteristics of the oftubulin protein or tubulin heterodimer. In particular, x-ray diffractionof a crystallized form of the of tubulin protein or tubulin heterodimercan be used to determine the three dimensional structure of the oftubulin protein or tubulin heterodimer.

Crystals of tubulin protein or tubulin heterodimer can be produced orgrown by a number of techniques including batch crystallization, vapordiffusion (either by sitting drop or hanging drop), soaking, and bymicrodialysis. Seeding of the crystals in some instances can be requiredto obtain x-ray quality crystals. Standard micro and/or macro seeding ofcrystals can be used. Preferably, the crystal diffracts x-rays for thedetermination of the atomic coordinates of the of tubulin protein ortubulin heterodimer to a resolution greater than 5.0 Angstroms,alternatively greater than 3.0 Angstroms, or alternatively greater than2.0

Crystals can be grown from a solution containing a purified tubulinprotein or tubulin heterodimer, or a fragment thereof (e.g., a stabledomain), by a variety of conventional processes (McPherson, 1982 JohnWiley, New York; McPherson, 1990, Eur. J. Biochem. 189: 1-23; Webber.1991, Adv. Protein Chem. 41:1-36). In some embodiments, native crystalsof the tubulin protein or tubulin heterodimer can be grown by addingprecipitants to the concentrated solution of the tubulin protein ortubulin heterodimer. The precipitants can be added at a concentrationjust below that necessary to precipitate the tubulin protein or tubulinheterodimer. Water can be removed by controlled evaporation to produceprecipitating conditions, which are maintained until crystal growthceases. The formation of crystals can depend on various factorsincluding pH, temperature, tubulin protein or tubulin heterodimerconcentration, the nature of the solvent and precipitant, as well as thepresence of added ions or ligands to the tubulin protein or tubulinheterodimer. In addition, the sequence of the tubulin protein or tubulinheterodimer being crystallized can have an effect on the success ofobtaining crystals. Many routine crystallization experiments can beneeded to screen all these factors for the few combinations that mightgive crystal suitable for x-ray diffraction analysis. Crystallizationrobots can automate and speed up the work of reproducibly setting uplarge number of crystallization experiments. Once the conditions forgrowing the crystal are optimized, variations of the condition can besystematically screened in order to find the set of conditions whichallow the growth of sufficiently large, single, well ordered crystals.In some embodiments, the tubulin protein or tubulin heterodimer can beco-crystallized with a compound that stabilizes the tubulin protein ortubulin heterodimer.

Before the data collection, the tubulin protein or tubulin heterodimercrystal can be frozen to protect it from radiation damage. A number ofdifferent cryo-protectants can be used to assist in freezing thecrystal, such as methyl pentanediol (MPD), isopropanol, ethylene glycol,glycerol, formate, citrate, mineral oil, or a low-molecular-weightpolyethylene glycol (PEG). As an alternative to freezing the crystal,the crystal can also be used for diffraction experiments performed attemperatures above the freezing point of the solution. In theseinstances, the crystal can be protected from drying out by placing it ina narrow capillary of a suitable material (generally glass or quartz)with some of the crystal growth solution included in order to maintainvapor pressure.

X-ray diffraction results can be recorded by a number of ways know toone of skill in the art. Examples of area electronic detectors includecharge coupled device detectors, multi-wire area detectors andphosphoimager detectors (Amemiya, Y, 1997. Methods in Enzymology, Vol.276. Academic Press, San Diego, pp. 233-243; Westbrook, E. M., Naday; 1.1997. Methods in Enzymology, Vol. 276. Academic Press, San Diego, pp.244-268; 1997. Kahn, R. & Fourme, R. Methods in Enzymology, Vol. 276.Academic Press, San Diego, pp. 268-286). Collection of X-ray diffractionpatterns are well known by those skilled in the art and are within thescope of the present invention.

Modeling of the three dimensional structure of the tubulin protein ortubulin heterodimer can be accomplished by either the crystallographerusing a computer graphics program such as TURBO or O (Jones, T A. etal., Acta Crystallogr. A47, 100-119, 1991) or, under suitablecircumstances, by using a fully automated model building program, suchas WARP (Anastassis et al. Nature Structural Biology, May 1999 Volume 6Number 5 pp 458-463) or MAID (Levitt, D. G., Acta Crystallogr. D 2001V57: 1013-9). This structure can be used to calculate model-deriveddiffraction amplitudes and phases.

The three dimensional structure of the crystal of the tubulin protein ortubulin heterodimer can be modeled using molecular replacement. The term“molecular replacement” refers to a method that involves generating apreliminary model of a molecule or complex whose structure coordinatesare unknown, by orienting and positioning a molecule whose structurecoordinates are known within the unit cell of the unknown crystal, so asbest to account for the observed diffraction pattern of the unknowncrystal. Phases can then be calculated from this model and combined withthe observed amplitudes to give an approximate Fourier synthesis of thestructure whose coordinates are unknown. This, in turn, can be subjectto any of the several forms of refinement to provide a final, moreaccurate structure of the unknown crystal.

Homology modeling (also known as comparative modeling or knowledge-basedmodeling) methods can also be used to develop a three dimensionalstructure of the tubulin protein or tubulin heterodimer. The methodutilizes a computer model of a known protein, a computer representationof the amino acid sequence of the polypeptide (e.g., tubulin protein ortubulin heterodimer) with an unknown structure, and standard computerrepresentations of the structures of amino acids. This method is wellknown to those skilled in the art (Greer, 1985, Science 228, 1055;Bundell et al 1988, Eur. J. Biochem. 172, 513).

A three dimensional structure of the tubulin protein or tubulinheterodimer can be described by the set of atoms that best predict theobserved diffraction data. Files can be created for the structure thatdefines each atom by its chemical identity, spatial coordinates in threedimensions, root mean squared deviation from the mean observed positionand fractional occupancy of the observed position. Hydrogen bonds andother atomic interactions, both within the protein and to bound ligands,can be identified. A model can represent the secondary, tertiary and/orquaternary structure of the tubulin protein or tubulin heterodimer. Themodel itself can be in two or three dimensions.

It is known in the art that a set of structure coordinates for aprotein, complex or a portion thereof, is a relative set of points thatdefine a shape in three dimensions. Thus, it is possible that anentirely different set of coordinates could define a similar oridentical shape. Moreover, slight variations in the individualcoordinates can have little effect on overall shape. Such variations incoordinates can be generated because ofmathematical manipulations of thestructure coordinates. For example, structure coordinates could bemanipulated by crystallographic permutations of the structurecoordinates, fractionalization of the structure coordinates, integeradditions or subtractions to sets of the structure coordinates,inversion of the structure coordinates or any combination of the above.

The three-dimensional structure of a tubulin protein or tubulinheterodimer, a known tubulin inhibitor or thyroid hormone/analogue, acandidate tubulin inhibitor, or a tubulin protein/tubulin heterodimerbound to a known tubulin inhibitor or thyroid hormone/analogue or acandidate tubulin inhibitor (tubulin protein-tubulin inhibitor complex),can be determined by conventional means as described above or as knownin the art. The structure factors from the three-dimensional structurecoordinates of tubulin protein or tubulin heterodimer can be utilized toaid the structure determination of the tubulin protein-tubulin inhibitorcomplex. Structure factors include mathematical expressions derived fromthree-dimensional structure coordinates of the tubulin protein ortubulin heterodimer. These mathematical expressions include, forexample, amplitude and phase information. The three-dimensionalstructure of the tubulin protein or tubulin heterodimer, a known tubulininhibitor or thyroid hormone/analogue, a candidate tubulin inhibitor ora tubulin protein or tubulin heterodimer-tubulin inhibitor complex canbe determined using molecular replacement analysis. This analysisutilizes a known three-dimensional structure as a search model todetermine the structure of a closely related tubulin protein or tubulinheterodimer, a known tubulin inhibitor or thyroid hormone/analogue, acandidate tubulin inhibitor or a tubulin protein or tubulinheterodimer-tubulin inhibitor complex.

In some embodiments, the tubulin protein or tubulin heterodimer can besoluble, purified and/or isolated tubulin protein or tubulin heterodimerwhich can optionally comprise a tag or label to facilitate expression,purification and/or structural or functional characterization. In someembodiments, a tubulin protein or tubulin heterodimer which is used inaccordance with the methods of the invention is labeled with an isotopiclabel to facilitate its detection and or structural characterizationusing nuclear magnetic resonance or another applicable technique.Exemplary isotopic labels include radioisotopic labels such as, forexample, potassium-40 (⁴⁰K), carbon-14 (¹⁴C), tritium (³H), sulfur-35(³⁵S), phosphorus-32 (³²P), technetium-99m (⁹⁹mTc), thallium-201(²⁰¹TI), gallium-67 (⁶⁷Ga), indium-111 (¹¹In), iodine-123 (¹²³I),iodine-131 (¹³¹I), yttrium-90 (⁹⁰Y), samarium-153 (¹⁵³Sm), rhenium-186(¹⁸⁶Re), rhenium-188 (¹⁸⁸Re), dysprosium-165 (¹⁶⁵Dy) and holmium-166(¹⁶⁶Ho). The isotopic label can also be an atom with non zero nuclearspin, including, for example, hydrogen-1 (¹H), hydrogen-2 (²H),hydrogen-3 (³H), phosphorous-31 (³¹P), sodium-23 (²³Na), nitrogen-14(¹⁴N), nitrogen-15 (¹⁵N), carbon-13 (¹³C) and fluorine-19 (¹⁹F).

In certain embodiments, the tubulin protein or tubulin heterodimer isuniformly labeled with an isotopic label, for example, wherein about50%, 70%, 80%, 90%, 95%, or 98% of the possible labels in the tubulinprotein or tubulin heterodimer are labeled, e.g., wherein about 50%,70%, 80%, 90%, 95%, or 98% of the nitrogen atoms in the tubulin proteinor tubulin heterodimer are ¹⁵N, and/or wherein about 50%, 70%, 80%, 90%,95%, or 98% of the carbon atoms in the tubulin protein or tubulinheterodimer are ¹³C, and/or wherein about 50%, 70%, 80%, 90%, 95%, or98% of the hydrogen atoms in the tubulin protein or tubulin heterodimerare ²H. In other embodiments, the isotopic label is located in one ormore specific locations within the tubulin protein or tubulinheterodimer. The invention also encompasses the embodiment wherein asingle tubulin protein or tubulin heterodimer comprises two or moredifferent isotopic labels, for example, the tubulin protein or tubulinheterodimer comprises both ¹⁵N and ¹³C labeling.

In yet another embodiment, the tubulin protein or tubulin heterodimerwhich can be used in accordance with the methods of the invention islabeled to facilitate structural characterization using x-raycrystallography or another applicable technique. Exemplary labelsinclude heavy atom labels such as, for example, cobalt, selenium,krypton, bromine, strontium, molybdenum, ruthenium, rhodium, palladium,silver, cadmium, tin, iodine, xenon, barium, lanthanum, cerium,praseodymium, neodymium, samarium, europium, gadolinium, terbium,dysprosium, holmium, erbium, thulium, ytterbium, lutetium, tantalum,tungsten, rhenium, osmium, iridium, platinum, gold, mercury, thallium,lead, thorium and uranium.

Designing a Tubulin Inhibitor

Designing as disclosed in the present invention involves designing achemical substance, particularly a candidate tubulin inhibitor thatinteracts in some way with receptor or binding domains of the tubulinprotein or tubulin heterodimer. Typically, for a drug to effectivelyinteract with the binding domains of the tubulin protein or tubulinheterodimer, it can be necessary that the three-dimensional shape(“conformation”) of tubulin protein or tubulin heterodimer assumes acompatible conformation that allows the drug and the binding domain ofthe tubulin protein or tubulin heterodimer to fit and bind together in away that produces a desired result. Preferably, the desired result is anefficient binding of the drug with the tubulin protein or tubulinheterodimer resulting in an inhibition of the tubulin activity. In suchinstance, the complex shape or conformation of the binding domain of thetubulin protein or tubulin heterodimer can be compared to a “lock”, andthe corresponding requisite shape or conformation of the drug as a “key”that unlocks (i.e., produces the desired result within) the bindingdomain of the tubulin protein or tubulin heterodimer. This“lock-and-key” analogy emphasizes that only a properly conformed key(drug patterned thereafter) is able to fit within the lock (the bindingdomain of the tubulin protein or tubulin heterodimer) in order to“unlock” it (produce a desired result). Further, even if the key fits inthe lock, it must have the proper composition in order for it to performits function. That is, the drug contains the elements in the spatialarrangement and position in order to properly bind with the bindingdomain of the tubulin protein or tubulin heterodimer. The design asdisclosed herein can include knowing or predicting the conformation ofthe binding domain of the tubulin protein or tubulin heterodimer, andalso controlling and/or predicting the conformation of the drug, i.e., acandidate tubulin inhibitor that is to interact with the binding domainof the tubulin protein or tubulin heterodimer.

Determination of the binding domain of the tubulin protein or tubulinheterodimer, and in particular the recognition of the role of domainshelps in identifying binding of tubulin inhibitors or thyroid hormoneanalogues in the binding domains of the tubulin protein or tubulinheterodimer. A known tubulin inhibitor or thyroid hormone analogue isused to evaluate its binding with the binding domain of the tubulinprotein or tubulin heterodimer. Based on this evaluation, computationaltechniques for drug design are used to design candidate tubulininhibitors based on the structure of a known tubulin inhibitor orthyroid hormone analogue. For example, automated ligand-receptor dockingprograms which require accurate information on the atomic coordinates oftarget receptors are used to design candidate tubulin inhibitors. Thecandidate tubulin inhibitors can be designed de novo or can be analogsof known tubulin inhibitors or thyroid hormone analogues. Preferably,the candidate tubulin inhibitor is designed based on a known tubulininhibitor or thyroid hormone analogue. More preferably, the candidatetubulin inhibitor is an analogue of thyroxine. Alternatively, thecandidate tubulin inhibitors can be synthesized and formed into acomplex with tubulin protein or tubulin protein heterodimer, and thecomplex can then be analyzed by x-ray crystallography to identify theactual position of the bound tubulin inhibitor. The structure and/orfunctional groups of the candidate tubulin inhibitor can then beadjusted, if necessary, in view of the results of the x-ray analysis,and the synthesis and analysis sequence repeated until an optimizedtubulin inhibitor is obtained.

The designing of the candidate tubulin inhibitor can involvecomputer-based in silico screening of compound databases (such as theCambridge structural database) with the aim of identifying compoundswhich interact with the binding cavity or sites of the target tubulinprotein or tubulin heterodimer. Screening selection criteria can bebased on pharmacokinetic properties such as metabolic stability andtoxicity. Determination of the mechanism of the tubulin inhibitionallows the architecture and the chemical nature of tubulin binding sitesto be better defined, which in turn allows the geometric and functionalconstraints of a substituent on the candidate tubulin inhibitor to bederived more accurately. The substituent can be a type of virtual 3-Dpharmacophore, which can be used as selection criteria or filter fordatabase screening.

In some preferred embodiments of the present invention, the candidatetubulin inhibitor is an analogue of thyroxine. Based on the interactionof the thyroxine with the binding domain of the tubulin protein ortubulin heterodimer, a candidate tubulin inhibitor can be designed.

In some embodiments, the compound is of formula I, its pharmaceuticallyacceptable salts or prodrugs thereof:

wherein: R₁ and R₅ are halogens; R₂, R₃, and R₄ are independentlyselected from the group consisting of hydrogen, hydroxyl, halogen,ester, optionally substituted alkoxy, optionally substituted amine,phosphate, optionally substituted alkyl, and optionally substitutedacetyl; R₆, R₇, R₈, R₉, and R₁₀ are independently selected from thegroup consisting of hydrogen, hydroxyl, halogen, optionally substitutedalkoxy, optionally substituted amine, phosphate, optionally substitutedalkyl, optionally substituted alkenyl, optionally substituted alkynyl,nitroso, carboxyl, optionally substituted cycloalkyl, and optionallysubstituted heterocyclic. The optionally substituted heterocyclic can befor example, azeridine, azetidine, pyrrole, dihydropyrrole, pyrrolidene,pyrazole, pyrazoline, pyrazolidine, imidazole, benzimidazole, triazole,tetrazole, oxazole, isoxazole, benzoxazole, oxadiazole, oxazoline,oxazolidine, thiazole, isothiazole, pyridine, dihydropyridine,tetrahydropyridine, quinazoline, pyrazine, pyrimidine, pyridazine,quinoline, isoquinoline, triazine, tetrazine, and piperazine.Preferably, the compounds as provided herein are tubulin inhibitors.

In some embodiments of the present invention, the compound is of formulaII, its pharmaceutically acceptable salts or prodrugs thereof:

wherein: R, R′, R₂, R₄, R₆, R₇, R₉, and R₁₀ are independently selectedfrom the group consisting of hydrogen, hydroxyl, halogen, optionallysubstituted alkoxy, optionally substituted amine, phosphate, optionallysubstituted alkyl, and optionally substituted acetyl. Preferably, thecompound is a tubulin inhibitor.

In some embodiments of the present invention, the compound is of formulaIII, its pharmaceutically acceptable salts or prodrugs thereof:

wherein R₆, R₇, R₉, and R₁₀ are independently selected from the groupconsisting of hydrogen, hydroxyl, optionally substituted amine,phosphate, and optionally substituted alkyl. Preferably, the compound isa tubulin inhibitor.

In some preferred embodiments, the compound is1-(4-(3-hydroxy-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone, representedby formula IIIA, its pharmaceutically acceptable salts or prodrugsthereof:

In some preferred embodiments, the compound is1-(4-(3-amino-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone, representedby formula IIIB, its pharmaceutically acceptable salts or prodrugsthereof:

In some preferred embodiments, the compound is1-(4-(2-amino-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone, representedby formula IIIC, its pharmaceutically acceptable salts or prodrugsthereof:

In some preferred embodiments, the compound is mono(5-methoxy-3-(4-acetyl-2,6-iodophenoxy)phenyl) phosphoric acid ester,represented by formula IIID, its pharmaceutically acceptable salts orprodrugs thereof:

In some preferred embodiments, the compound is1-(4-(2-(N-piperazinylprop-3-yl))-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone,represented by formula IIIE, its pharmaceutically acceptable salts orprodrugs thereof:

Typical salts are those of the inorganic ions, such as, for example,sodium, potassium, calcium, magnesium ions, and the like. Such saltsinclude salts with inorganic or organic acids, such as hydrochloricacid, hydrobromic acid, phosphoric acid, nitric acid, sulfuric acid,methanesulfonic acid, p-toluenesulfonic acid, acetic acid, turmericacid, succinic acid, lactic acid, mandelic acid, malic acid, citricacid, tartaric acid or maleic acid. In addition, if the compound(s)contain a carboxy group or other acidic group, it can be converted intoa pharmaceutically acceptable addition salt with inorganic or organicbases. Examples of suitable bases include sodium hydroxide, potassiumhydroxide, ammonia, cyclohexylamine, dicyclohexyl-amine, ethanolamine,diethanolamine, triethanolamine, and the like.

The candidate tubulin inhibitors described herein can contain one ormore asymmetric centers and thus occur as racemates and racemicmixtures, single enantiomers, individual diastereomers anddiastereomeric mixtures. All such isomeric forms of these compounds areexpressly included in the present invention. The tubulin inhibitorsdescribed herein can also be represented in multiple tautomeric forms,all of which are included herein. The tubulin inhibitors can also occurin cis- or trans- or E- or Z-double bond isomeric forms. All suchisomeric forms of such inhibitors are expressly included in the presentinvention. All crystal forms of the tubulin inhibitors described hereinare expressly included in the present invention. The tubulin inhibitorscan also be present as their pharmaceutically acceptable salts,derivatives or prodrugs.

The known or a candidate tubulin inhibitor molecule or thyroid analoguecan be examined through the use of computer modeling using a dockingprogram such as GRID, DOCK, or AUTODOCK (see Wolfgang B. Fischer, Anal.Bioanal. Chem. 2003, 375, 23-25). This procedure can include computerfitting of a three dimensional structure of a known or a candidatetubulin inhibitor molecule to a binding domain of the tubulin protein ortubulin heterodimer to ascertain how well the shape and the chemicalstructure of the known or the candidate tubulin inhibitor molecule willcomplement the binding domain of the tubulin protein or tubulinheterodimer. Computer programs can also be employed to estimate theattraction, repulsion, and steric hindrance of the known or thecandidate tubulin inhibitor to the binding domain of the tubulin proteinor tubulin heterodimer. Typically, the tighter the fit (e.g., the lowerthe steric hindrance, and/or the greater the attractive force) the morepotent the tubulin inhibitor will be since these properties areconsistent with a tighter binding constant. Furthermore, the morespecificity in the design of a candidate tubulin inhibitor the morelikely it can be that the candidate tubulin inhibitor will not interferewith other properties of the tubulin protein or tubulin heterodimer orother proteins. This can minimize potential side-effects due to unwantedinteractions with other proteins.

Numerous computer programs are available and suitable for a drug designand the processes of computer modeling, model building, andcomputationally identifying, selecting and evaluating candidate tubulininhibitors in the methods described herein. These include, for example,GRID (available form Oxford University, UK), MCSS (available fromMolecular Simulations Inc., Burlington, Mass.), AUTODOCK (available fromOxford Molecular Group), FLEX X (available from Tripos, St. Louis. Mo.),DOCK (available from University of California, San Francisco), CAVEAT(available from University of California, Berkeley), HOOK (availablefrom Molecular Simulations Inc., Burlington, Mass.), and 3D databasesystems such as MACCS-3D (available from MDL Information Systems, SanLeandro, Calif.), UNITY (available from Tripos, St. Louis. Mo.), andCATALYST (available from Molecular Simulations Inc., Burlington, Mass.).The computer program that can be used in the present invention is ICM(available from Molsoft L L C, La Jolla, Calif.).

Potential tubulin inhibitors can also be computationally designed “denovo” using such software packages as LUDI (available from BiosymTechnologies, San Diego, Calif.), LEGEND (available from MolecularSimulations Inc., Burlington, Mass.), and LEAPFROG (Tripos Associates,St. Louis, Mo.). Compound deformation energy and electrostaticrepulsion, can be evaluated using programs such as GAUSSIAN 92, AMBER,QUANTA/CHARMM, AND INSIGHT II/DISCOVER. These computer evaluation andmodeling techniques can be performed on any suitable hardware includingfor example, workstations available from Silicon Graphics, SunMicrosystems, and the like. The computer workstation that can be used inthe present invention is Apple Power Mac G5. The techniques, methods,hardware and software as disclosed herein are representative and are notintended to be limiting to the scope of the present invention. Othermodeling techniques known in the art can also be employed in accordancewith this invention.

Another aspect of the invention relates to a computer system containinga set of information to perform a design of a tubulin inhibitor having auser interface comprising a display unit, the set of informationcomprising:

-   -   a) logic for inputting an information regarding a binding of a        tubulin protein to a chemical known to bind tubulin protein;    -   b) logic for designing a candidate tubulin inhibitor based on        the binding of the tubulin protein to the chemical known to bind        tubulin protein;    -   c) logic for determining an information regarding a binding of        the tubulin protein to the candidate tubulin inhibitor; and    -   d) logic for making a conclusion regarding a tubulin inhibitory        properties of the candidate tubulin inhibitor based on the        determination of step c).

In some preferred embodiments, the steps of the methods of the presentinvention are performed using a computer as depicted in FIG. 2. FIG. 2illustrates a computer for implementing selected operations associatedwith the methods of the present invention. The computer 200 includes acentral processing unit 201 connected to a set of input/output devices202 via a system bus 203. The input/output devices 202 can include akeyboard, mouse, scanner, data port, video monitor, liquid crystaldisplay, printer, and the like. A memory 204 in the form of primaryand/or secondary memory is also connected to the system bus 203. Thesecomponents of FIG. 2 characterize a standard computer. This standardcomputer is programmed in accordance with the invention. In particular,the computer 200 can be programmed to perform various operations of themethods of the present invention.

The memory 204 of the computer 200 can store a modeling/determiningmodule 205. In other words, the modeling/determining module 205 canperform the operations associated with steps of FIG. 1. Themodeling/determining module includes modeling a three dimensionalstructure of tubulin protein or tubulin heterodimer from a crystal ofthe tubulin protein or tubulin heterodimer, modeling a three dimensionalstructure of a binding domain of a tubulin protein or tubulinheterodimer, modeling a three dimensional structure of a known tubulininhibitor or thyroid hormone analogue, modeling and determining abinding of the three dimensional structure of the binding domain of atubulin protein or tubulin heterodimer with the tubulin inhibitor orthyroid hormone analogue, modeling a three dimensional structure of acandidate tubulin inhibitor, modeling and determining a binding of thethree dimensional structure of the binding domain of the tubulin proteinor tubulin heterodimer with the candidate tubulin inhibitor, andevaluating the binding of the known tubulin inhibitor or thyroid hormoneanalogue or the candidate tubulin inhibitor with the tubulin protein ortubulin heterodimer. The modeling module can also include a conclusionmodule which includes a conclusion regarding the candidate tubulininhibitor that inhibits tubulin activity.

The candidate tubulin inhibitor as disclosed herein can be prepared byemploying standard synthetic techniques known in the art. The candidatetubulin inhibitors can be analyzed for their bioactivity. Preferably,the bioactivity relates to inhibition of tubulin activity. The compoundswhich display tubulin inhibiting activity can be candidate tubulininhibitors, while the compounds which do not display tubulin inhibitingactivity help define portions of the molecule which are particularlyinvolved in imparting tubulin inhibiting activity to the candidatetubulin inhibitor. Where analogue compounds are not bioactive,additional analogue compounds can be designed, subjected to the methodsof the present invention, and then tested for bioactivity. Additionalcandidate tubulin inhibitors can be devised by either repeating theabove-described process, or seeking to render other portions of thetarget structure chemically modified.

In some embodiments of the present invention, pertinent physical andchemical properties (i.e., sites of hydrogen bonding, surface area,atomic and molecular volume, charge density, directionality of thecharges, etc.) of candidate tubulin inhibitors can be used to develop acollection of parameters required for the desired bioactivity. Adatabase of known compounds (e.g., the Cambridge crystal structuredatabase) can then be searched for structures which contain the stericparameters required for the desired bioactivity. Compounds which arefound to contain the desired steric parameters can be retrieved, andfurther analyzed to determine which of the retrieved compounds also havethe desired electronic properties, relative to the candidate tubulininhibitor. Compounds that are found to contain both the desired stericand electronic properties can be additional candidates as tubulininhibitors.

Known compounds which also possess the collection of parameters requiredfor the desired bioactivity can then be tested to see if they alsopossess the desired bioactivity. Alternatively, known compounds whichalso possess the collection of parameters required for the desiredbioactivity can be modified to remove excess functionality which is notrequired for the particular bioactivity being tested. Such a modifiedcompound can be a simple, readily prepared tubulin inhibitor.

The tubulin inhibitors described herein are also useful for inhibitingthe biological activity of any protein comprising greater than 90%,alternatively greater than 85%, or alternatively greater than 70%sequence homology with a tubulin protein sequence. The tubulininhibitors described herein are also useful for inhibiting thebiological activity of any protein comprising a subsequence, or variantthereof, of any protein that comprises greater than 90%, alternativelygreater than 85%, or alternatively greater than 70% sequence homologywith a tubulin subsequence. Such subsequence preferably comprisesgreater than 90%, alternatively greater than 85%, or alternativelygreater than 70% sequence homology with the sequence of an active siteor subdomain of a tubulin protein.

Synthesis Schemes for Candidate Tubulin Inhibitors

The candidate tubulin inhibitor s as disclosed herein can be prepared byemploying standard synthetic techniques known in the art and suchtechniques are within the scope of the present invention. Withoutlimiting the scope of the present invention some of the synthesisschemes for the candidate Tubulin inhibitor s are provided as below.

An example of a synthesis scheme for candidate tubulin inhibitor of acompound of formula IIIA from pyrocatechol (CAS 120-80-9) is as providedbelow (Evans D. A. et al., J. Am. Chem. Soc. 2001, 123, 12411-12413;Evans D. A. et al., Tetrahedron Lett. 1998, 39, 2933-2936; Saimoto H. etal., Tetrahedron Lett., 1986, 27, 1607; Covello M. et. al., Chem. Abstr.1962, 56, 5929i).

An alternate synthesis of a compound of formula IIIA starts with acompound of formula IIIB, which is first converted to a diazonium saltin the presence of a metal nitrate, such as sodium nitrate. Thisnitronium ion is then transformed into the hydroxy by reflux in thepresence of a strong acid, such as sulfuric acid.

First, the compound of formula IIIB is obtained as described herein andis suspended in 6 N sulfuric acid. The reaction mixture is cooled toTi=0-5° C. Sodium nitrate is dissolved in water and is added dropwiseunder the surface of the starting material suspension. As the suspensionis very thick, further water is added and stirring is continued for 2.5hour at Ti=0-5° C. Further sodium nitrate is added and stirring iscontinued for 3 hours. A few crystals of urea are added to decompose anyexcess sodium nitrate. Test with iodine-starch paper.

The diazonium suspension is added to pre-heated 6N sulfuric acid within1 hour. Heating is continued for 24 hours. The suspension is cooled toroom temperature and filtered off and washed with water. The solid isdried in vacuo at 40° C. The crude product may be purified bychromatography on silica gel.

An example of a synthesis scheme for candidate tubulin inhibitor of acompound of formula IIIB from 4-bromoanisole (CAS 104-92-7) is asprovided below (Evans D. A. et al., J. Am. Chem. Soc. 2001, 123,12411-12413; Evans D. A. et al., Tetrahedron Lett. 1998, 39, 2933-2936;Muathen H. A., Molecules, 2003, 8, 593-598; Saimoto H. et al.,Tetrahedron Lett., 1986, 27, 1607; Hantson A. L. et al., 5^(th)International Conference on Isotopes, Brussels, Belgium, Apr. 25-29,2005, 279-283; Covello M. et. al., Chem. Abstr. 1962, 56, 5929i).

An alternate synthetic scheme for a compound of formula IIIB is beginswith 1-(3,5-diiodo-4-(4-methoxyphenoxy)phenyl)ethanone (DIPE) asstarting material. First, DIPE is nitrated to form a 3-nitro adduct. Thenitration may be carried out in a suitable reagent, such as nitric acid,e.g. in the presence of a strong acid such as sulfuric acid. Once the3-nitro adduct (nitro intermediate) has been formed, it can then bereduced to form the 3-amino adduct, which is the compound of formulaIIIB.

The reduction of the nitro intermediate must be carried out with areducing reagent that will selectively reduce the aryl nitro moiety butnot the aryl carbonyl moiety. It has been found that tin(II) chloride(SnCl₂) in 37% HCl is such a reagent; however other reagent systems thatreduce the nitro moiety and spare the aryl carbonyl moiety may beemployed. In some embodiments it may be critical to choose a reagentsuch as SnCl₂/HCl that gives a nearly quantitative (>95% or >97.5%, >99%purity) conversion of 3-nitro to 3-amino moiety.

In step 1, DIPE is first dissolved in methylene chloride. A solution ofnitric acid and sulfuric acid is cooled to Ti −0-5° C. The acid mixtureis added to the starting material solution at Ti<5° C. A solution of thenitro-intermediate is obtained. The reaction mixture is then dilutedwith methylene chloride until solids dissolve completely. The organicphase is washed with water, 10% aqueous sodium bicarbonate solution andthen water. The organic phase is dried over sodium sulfate andconcentrated in vacuo.

In step 2, a solution of ethanol and 37% HCl is cooled to Ti<10° C., towhich is added anhydrous tin(II) chloride. This produces a clear,colorless solution. The nitro intermediate is then added immediately.The ice bath is removed and the suspension is warmed to room temperaturewithin 30 min. The suspension is then warmed to Ti=30-35° C. Thisreaction mixture is then stirred at room temperature overnight. Thereaction mixture is then filtered and the filtrate washed with ethanoland dried in vacuo at 38° C. The crude product may then bere-crystallized from TBME.

An example of a synthesis scheme for candidate tubulin inhibitor of acompound of formula IIIC from 1-iodo-4-methoxy-2-nitrobenzene (CAS50590-07-3) is as provided below (Beringer et al. JACS, 1959, 81, 343;Organic Syntheses, 1995, Coll. Vol. 3, p. 355; 1942, Vol. 22, p. 52;Hantson A. L. et al., 5^(th) International Conference on Isotopes,Brussels, Belgium, Apr. 25-29, 2005, 279-283; Gowda D. et al., Ind. J.Chem. Sect. B, 2001, 40, 75-77; Covello M. et. al., Chem. Abstr. 1962,56, 5929i).

An example of a synthesis scheme for candidate tubulin inhibitor of acompound of formula IIID from pyrocatechol (CAS 120-80-9) is as providedbelow (Evans D. A. et al., J. Am. Chem. Soc. 2001, 123, 12411-12413;Evans D. A. et al., Tetrahedron Lett. 1998, 39, 2933-2936; Perich J. W.et al., Synthesis 1988, 142-144; Covello M. et. al., Chem. Abstr. 1962,56, 5929i).

An example of a synthesis scheme for candidate tubulin inhibitor of acompound of formula IIIE from 3-(3-methoxyphenyl)proprionic acid (CAS10516-71-9) is as provided below (Beringer et al., JACS, 1959, 81, 343;Organic Syntheses, 1995, Coll. Vol. 3, p. 355; 1942, Vol. 22, p. 52;Wing-Wah Sy, Tetrahedron Lett. 1993, 39, 6223-6224; Hantson A. L. etal., 5^(th) International Conference on Isotopes, Brussels, Belgium,Apr. 25-29, 2005, 279-283; Covello M. et. al., Chem. Abstr. 1962, 56,5929i; B. W. Yoo et. al., Bull. Korean Chem. Soc. 2004, Vol. 25, No. 11,1633-1634).

Techniques for the Measurement of Tubulin Inhibiting Activity of TubulinInhibitors

In some embodiments, a tubulin inhibiting activity of the candidatetubulin inhibitor is evaluated to characterize the ability of acandidate tubulin inhibitor to bind to a tubulin protein or tubulinheterodimer, and/or characterize the ability of the candidate tubulininhibitor to modify the activity of a tubulin protein or tubulinheterodimer. Preferably, the technique used for evaluation is an assaytechnique. Both in vitro and in vivo assays can be used in accordancewith the methods of the invention depending on the identity of thetubulin protein or tubulin heterodimer being investigated. Appropriateactivity or functional assays can be readily determined by the skilledartisan based on the disclosure herein. The candidate tubulin inhibitorsdescribed herein can be used in assays, including radiolabeled, antibodydetection and fluorometric assays, for the isolation, identification, orstructural or functional characterization of the tubulin protein ortubulin heterodimer.

The assay can be an enzyme inhibition assay or tubulin inhibition assayutilizing a full length or truncated tubulin protein or tubulinheterodimer. The tubulin protein or tubulin heterodimer can be contactedwith the candidate tubulin inhibitor and a measurement of the bindingaffinity of the candidate tubulin inhibitor against a standard isdetermined. Such assays are known to one of ordinary skill in the artand are within the scope of the present invention. The assay forevaluating tubulin inhibiting activity of the candidate tubulininhibitor can be a cell-based assay. The candidate tubulin inhibitor iscontacted with a cell and a measurement of an inhibition of a standardmarker produced in the cell is determined. Cells can be either isolatedfrom an animal, including a transformed cultured cell, or can be in aliving animal. Such assays are also known to one of ordinary skill inthe art and are within the scope of the present invention.

The candidate tubulin inhibitors of the present invention can beidentified using, for example, immunoassays such as enzyme linkedimmunoabsorbent assays (ELISA) and radioimmunoassays (RIA) or bindingassays such as Biacore assays. Binding assays can employ kinetic orthermodynamic methodology using a wide variety of techniques including,but not limited to, microcalorimetry, circular dichroism, capillary zoneelectrophoresis, nuclear magnetic resonance spectroscopy, fluorescencespectroscopy, and combinations thereof. Without limiting the scope ofthe present invention, some of the examples of the techniques formeasurement of the bioactivity of the tubulin inhibitors, are providedbelow.

Fluorescence Microscopy

Some embodiments of the invention include fluorescence microscopy formeasuring the tubulin inhibiting activity of the candidate tubulininhibitors of the present invention. Fluorescence microscopy enables themolecular composition of the structures being observed to be identifiedthrough the use of fluorescently-labeled probes of high chemicalspecificity such as antibodies. It can be done by directly conjugating afluorophore to a tubulin protein or tubulin heterodimer and introducingthis back into a cell. Fluorescent analogue can behave like the nativeprotein and can therefore serve to reveal the distribution and behaviorof this tubulin protein or tubulin heterodimer in the cell. Along withNMR, infrared spectroscopy, circular dichroism and other techniques,protein intrinsic fluorescence decay and its associated observation offluorescence anisotropy, collisional quenching and resonance energytransfer are techniques for tubulin detection. The naturally fluorescentproteins can be used as fluorescent probes. The jellyfish Aequoreavictoria produces a naturally fluorescent protein known as greenfluorescent protein (GFP). The fusion of these fluorescent probes to atarget protein enables visualization by fluorescence microscopy andquantification by flow cytometry.

By way of example only, some of the probes are labels such as,fluorescein and its derivatives, carboxyfluoresceins, rhodamines andtheir derivatives, atto labels, fluorescent red and fluorescent orange:cy3/cy5 alternatives, lanthanide complexes with long lifetimes, longwavelength labels—up to 800 rn, DY cyanine labels, and phycobiliproteins. By way of example only, some of the probes are conjugates suchas, isothiocyanate conjugates, streptavidin conjugates, and biotinconjugates. By way of example only, some of the probes are enzymesubstrates such as, fluorogenic and chromogenic substrates. By way ofexample only, some of the probes are fluorochromes such as, FITC (greenfluorescence, excitation/emission=506/529 nm), rhodamine B (orangefluorescence, excitation/emission=560/584 nm), and Nile blue A (redfluorescence, excitation/emission=636/686 nm). Fluorescent nanoparticlescan be used for various types of immunoassays. Fluorescent nanoparticlesare based on different materials, such as, polyacrylonitrile, andpolystyrene etc. Fluorescent molecular rotors are sensors ofmicroenvironment restriction that become fluorescent when their rotationis constrained. Few examples of molecular constraint include increaseddye (aggregation), binding to antibodies, or being trapped in thepolymerization of actin. IEF (isoelectric focusing) is an analyticaltool for the separation of ampholytes, mainly proteins. An advantage forIEF-gel electrophoresis with fluorescent IEF-marker is the possibilityto directly observe the formation of gradient. Fluorescent IEF-markercan also be detected by UV-absorption at 280 nm (20° C.).

A peptide library can be synthesized on solid supports and, by usingcoloring receptors, subsequent dyed solid supports can be selected oneby one. If receptors cannot indicate any color, their binding antibodiescan be dyed. The method can not only be used on protein receptors, butalso on screening binding ligands of synthesized artificial receptorsand screening new metal binding ligands as well. Automated methods forHTS and FACS (fluorescence activated cell sorter) can also be used.

Immunoassays

Some embodiments of the invention include immunoassay for measuring thetubulin inhibiting activity of the candidate tubulin inhibitors of thepresent invention. In immunoblotting like the western blot ofelectrophoretically-separated proteins a single protein can beidentified by its antibody. An immunoassay can be a competitive bindingimmunoassay where analyte competes with a labeled antigen for a limitedpool of antibody molecules (e.g. radioimmunoassay, EMIT). An immunoassaycan be non-competitive where an antibody is present in excess and islabeled. As analyte antigen complex is increased, the amount of labeledantibody-antigen complex can also increase (e.g. ELISA). Antibodies canbe polyclonal if produced by antigen injection into an experimentalanimal, or monoclonal if produced by cell fusion and cell culturetechniques. In an immunoassay, the antibody can serve as a specificreagent for the analyte antigen.

Without limiting the scope and content of the present invention, some ofthe types of immunoassays are, but not limited to, RIAs(radioimmunoassay), enzyme immunoassays like ELISA (enzyme-linkedimmunosorbent assay), EMIT (enzyme multiplied immunoassay technique),microparticle enzyme immunoassay (MEIA), LIA (luminescent immunoassay),and FIA (fluorescent immunoassay). The antibodies—either used as primaryor secondary ones—can be labeled with radioisotopes (e.g. 125I),fluorescent dyes (e.g. FITC) or enzymes (e.g. HRP or AP) which cancatalyze fluorogenic or luminogenic reactions.

Biotin, or vitamin H is a co-enzyme which inherits a specific affinitytowards avidin and streptavidin. This interaction makes biotinylatedpeptides a useful tool in various biotechnology assays for quality andquantity testing. To improve biotin/streptavidin recognition byminimizing steric hindrances, it can be necessary to enlarge thedistance between biotin and the peptide itself. This can be achieved bycoupling a spacer molecule (e.g., 6-aminohexanoic acid) between biotinand the peptide.

The biotin quantitation assay for biotinylated proteins provides asensitive fluorometric assay for accurately determining the number ofbiotin labels on a protein. Biotinylated peptides are widely used in avariety of biomedical screening systems requiring immobilization of atleast one of the interaction partners onto streptavidin coated beads,membranes, glass slides or microtiter plates. The assay is based on thedisplacement of a ligand tagged with a quencher dye from the biotinbinding sites of a reagent. To expose any biotin groups in amultiply-labeled protein that are sterically restricted and inaccessibleto the reagent, the protein can be treated with protease for digestingthe protein.

EMIT is a competitive binding immunoassay that avoids the usualseparation step. A type of immunoassay in which the protein is labeledwith an enzyme, and the enzyme-protein-antibody complex is enzymaticallyinactive, allowing quantitation of unlabelled protein. Some embodimentsof the invention include ELISA to analyze tubulin proteins or tubulinheterodimers. ELISA is based on selective antibodies attached to solidsupports combined with enzyme reactions to produce systems capable ofdetecting low levels of proteins. It is also known as enzyme immunoassayor EIA. The protein is detected by antibodies that have been madeagainst it, that is, for which it is the antigen. Monoclonal antibodiesare often used.

The test can require the antibodies to be fixed to a solid surface, suchas the inner surface of a test tube, and a preparation of the sameantibodies coupled to an enzyme. The enzyme can be one (e.g.,β-galactosidase) that produces a colored product from a colorlesssubstrate. The test, for example, can be performed by filling the tubewith the antigen solution (e.g., protein) to be assayed. Any antigenmolecule present can bind to the immobilized antibody molecules. Theantibody-enzyme conjugate can be added to the reaction mixture. Theantibody part of the conjugate binds to any antigen molecules that werebound previously, creating an antibody-antigen-antibody “sandwich”.After washing away any unbound conjugate, the substrate solution can beadded. After a set interval, the reaction is stopped (e.g., by adding 1N NaOH) and the concentration of colored product formed is measured in aspectrophotometer. The intensity of color is proportional to theconcentration of bound antigen.

ELISA can also be adapted to measure the concentration of antibodies, inwhich case, the wells are coated with the appropriate antigen. Thesolution (e.g., serum) containing antibody can be added. After it hashad time to bind to the immobilized antigen, an enzyme-conjugatedanti-immunoglobulin can be added, consisting of an antibody specific forthe antibodies being tested for. After washing away unreacted reagent,the substrate can be added. The intensity of the color produced isproportional to the amount of enzyme-labeled antibodies bound (and thusto the concentration of the antibodies being assayed).

Some embodiments of the invention include radioimmunoassays formeasuring the tubulin inhibiting activity of the candidate tubulininhibitors of the present invention. Radioactive isotopes can be used tostudy in vivo metabolism, distribution, and binding of small amount ofcompounds. Radioactive isotopes of ¹H, ¹²C, ³¹P, ³²S, and ¹²⁷I, in bodyare used such as ³H, ¹⁴C, ³²P, ³⁵S, and ¹²⁵I. In receptor fixationmethod in 96 well plates, receptors can be fixed in each well by usingantibody or chemical methods and radioactive labeled ligands can beadded to each well to induce binding. Unbound ligands can be washed outand then the standard can be determined by quantitative analysis ofradioactivity of bound ligands or that of washed-out ligands. Then,addition of screening target compounds can induce competitive bindingreaction with receptors. If the compounds show higher affinity toreceptors than standard radioactive ligands, most of radioactive ligandswould not bind to receptors and can be left in solution. Therefore, byanalyzing quantity of bound radioactive ligands (or washed-out ligands),testing compounds' affinity to receptors can be indicated.

The filter membrane method can be needed when receptors cannot be fixedto 96 well plates or when ligand binding needs to be done in solutionphase. In other words, after ligand-receptor binding reaction insolution, if the reaction solution is filtered through nitrocellulosefilter paper, small molecules including ligands can go through it andonly protein receptors can be left on the paper. Only ligands thatstrongly bound to receptors can stay on the filter paper and therelative affinity of added compounds can be identified by quantitativeanalysis of the standard radioactive ligands.

Some embodiments of the invention include fluorescence immunoassays formeasuring the tubulin inhibiting activity of the candidate tubulininhibitors of the present invention. Fluorescence based immunologicalmethods are based upon the competitive binding of labeled ligands versusunlabeled ones on highly specific receptor sites. The fluorescencetechnique can be used for immunoassays based on changes in fluorescencelifetime with changing analyte concentration. This technique can workwith short lifetime dyes like fluorescein isothiocyanate (FITC) (thedonor) whose fluorescence can be quenched by energy transfer to eosin(the acceptor). A number of photoluminescent compounds can be used, suchas cyanines, oxazines, thiazines, porphyrins, phthalocyanines,fluorescent infrared-emitting polynuclear aromatic hydrocarbons,phycobiliproteins, squaraines and organo-metallic complexes,hydrocarbons and azo dyes.

Fluorescence-based immunological methods can be, for example,heterogeneous or homogenous. Heterogeneous immunoassays comprisephysical separation of bound from free labeled analyte. The analyte orantibody can be attached to a solid surface. Homogenous immunoassayscomprise no physical separation. Double-antibody fluorophore-labeledantigen participates in an equilibrium reaction with antibodies directedagainst both the antigen and the fluorophore. Labeled and unlabeledantigen can compete for a limited number of anti-antigen antibodies.

Some of the fluorescence immunoassay methods include simple fluorescencelabeling method, fluorescence resonance energy transfer (FRET), timeresolved fluorescence (TRF), and scanning probe microscopy (SPM). Thesimple fluorescence labeling method can be used for receptor-ligandbinding, enzymatic activity by using pertinent fluorescence, and as afluorescent indicator of various in vivo physiological changes such aspH, ion concentration, and electric pressure.

Method of Treatment with Tubulin Inhibitors

The present invention relates to a pharmaceutical composition,medicament, drug, or other composition of the candidate tubulininhibitors comprising compounds of formulae I-III where III includesIIIA-E, for treatment of diseases. Preferably, the diseases aretubulin-mediated diseases. The candidate tubulin inhibitors of thepresent invention can have therapeutic benefit in the treatment ofvarious diseases including cancer and metabolic diseases, and as anadjunct therapy with chemotherapeutic agents/radiation in therapy forcancer.

The methods of the present invention also comprise administering one ormore the candidate tubulin inhibitors in combination with othertherapies. The condition being treated will determine the type oftherapy that will be co-administered with the candidate tubulininhibitors. For example, for treating cancer, the compound of someembodiments of the invention can be used in combination with antibody(polyclonal or monoclonal) therapy, chemotherapy, radiation therapy,bone marrow transplantation, side-effect-limiting therapy, nucleotidetherapy, gene therapy, or a combination thereof.

In addition, the candidate tubulin inhibitors can be used to treat avariety of diseases including metabolic diseases. Such diseases,include, but are not limited to, gout.

In another aspect of the invention, the candidate tubulin inhibitors canbe utilized to treat cancer, and to radiosensitize and/or chemosensitizecancer cells. The candidate tubulin inhibitors of the present inventioncan be “anticancer agents,” which term also encompasses “anti-tumor cellgrowth agents,” “pro-differentiating reagents,” “anti-angiogenicagents,” “pro-angiogenic agents,” “anti-mitotic agents,”“anti-proliferative agents,” “pro-apoptotic agents,” “anti-vascularagents,” and “pro-necrotic agents.” Radiosensitizers are known toincrease the sensitivity of cancerous cells to the toxic effects ofelectromagnetic radiation of x-rays. Examples of x-ray activatedradiosensitizers include, but are not limited to, the following:metronidazole, misonidazole, desmethylmisonidazole, pimonidazole,etanidazole, nimorazole, mitomycin C, RSU 1069, SR 4233, E09, RB 6145,nicotinamide, 5-bromodeoxyuridine (BrDU), 5-iododeoxyuridine (IUdR),bromodeoxycytidine, fluorodeoxyuridine (FudR), hydroxyurea, cisplatin,and therapeutically effective analogs and derivatives of the same.

Photodynamic therapy (PDT) of cancers employs visible light as theradiation activator of the sensitizing agent. Examples of photodynamicradiosensitizers include the following, but are not limited to:hematoporphyrin derivatives, photofrin, benzoporphyrin derivatives,NPe6, tin etioporphyrin SnET2, pheoborbide-α, bacteriochlorophyll-α,naphthalocyanines, phthalocyanines, zinc phthalocyanine, andtherapeutically effective analogs and derivatives of the same.

Chemosensitizers are also known to increase the sensitivity of cancerouscells to the toxic effects of chemotherapeutic compounds. Exemplarychemotherapeutic agents that can be used in conjunction with candidatetubulin inhibitors include, but are not limited to, adriamycin,camptothecin, dacarbazine, carboplatin, cisplatin, daunorubicin,docetaxel, doxorubicin, interferon (alpha, beta, ganma), interleukin 2,innotecan, paclitaxel, streptozotocin, temozolomide, topotecan, andtherapeutically effective analogs and derivatives of the same. Inaddition, other therapeutic agents which can be used in conjunction withcandidate tubulin inhibitors include, but are not limited to,5-fluorouracil, leucovorin, 5′-amino-5′-deoxythymidine, oxygen,carbogen, red cell transfusions, perfluorocarbons (e.g., Fluosol-DA),2,3-DPG, BW12C, calcium channel blockers, pentoxyfylline,antiangiogenesis compounds, hydralazine, and L-BSO.

The methods of treatment as disclosed herein can be via oraladministration, transmucosal administration, buccal administration,nasal administration, inhalation, parental administration, intravenous,subcutaneous, intramuscular, sublingual, transdermal administration, andrectal administration.

Pharmaceutical compositions of the candidate tubulin inhibitors of thepresent invention, include compositions wherein the active ingredient iscontained in a therapeutically or prophylactically effective amount,i.e., in an amount effective to achieve therapeutic or prophylacticbenefit. The actual amount effective for a particular application willdepend, inter alia, on the condition being treated and the route ofadministration. Determination of an effective amount is well within thecapabilities of those skilled in the art. The pharmaceuticalcompositions comprise the candidate tubulin inhibitor, one or morepharmaceutically acceptable carriers, diluents or excipients, andoptionally additional therapeutic agents. The compositions can beformulated for sustained or delayed release.

A preferred therapeutic composition of the present invention alsoincludes an excipient, an adjuvant and/or carrier. Suitable excipientsinclude compounds that the subject to be treated can tolerate. Examplesof such excipients include water, saline, Ringer's solution, dextrosesolution, Hank's solution, and other aqueous physiologically balancedsalt solutions. Nonaqueous vehicles, such as fixed oils, sesame oil,ethyl oleate, or triglycerides can also be used. Other usefulformulations include suspensions containing viscosity enhancing agents,such as sodium carboxymethylcellulose, sorbitol, or dextran. Excipientscan also contain minor amounts of additives, such as substances thatenhance isotonicity and chemical stability. Examples of buffers includephosphate buffer, bicarbonate buffer and Tris buffer, while examples ofpreservatives include thimerosal, o-cresol, formalin and benzyl alcohol.Standard formulations can either be liquid injectables or solids whichcan be taken up in a suitable liquid as a suspension or solution forinjection. Thus, in a non-liquid formulation, the excipient can comprisedextrose, human serum albumin, preservatives, etc., to which sterilewater or saline can be added prior to administration. In one embodimentof the present invention, a therapeutic composition can include acarrier. Carriers include compounds that increase the half-life of atherapeutic composition in the treated subject. Suitable carriersinclude, but are not limited to, polymeric controlled release vehicles,biodegradable implants, liposomes, bacteria, viruses, other cells, oils,esters, and glycols.

The oral form in which the therapeutic agent is administered can includepowder, tablet, capsule, solution, or emulsion. The effective amount canbe administered in a single dose or in a series of doses separated byappropriate time intervals, such as hours. Pharmaceutical compositionscan be formulated in conventional manner using one or morephysiologically acceptable carriers comprising excipients andauxiliaries which facilitate processing of the active compounds intopreparations which can be used pharmaceutically. Proper formulation isdependent upon the route of administration chosen. Suitable techniquesfor preparing pharmaceutical compositions of the therapeutic agents ofthe present invention are well known in the art.

It will be appreciated that appropriate dosages of the active compounds,and compositions comprising the active compounds, can vary from patientto patient. Determining the optimal dosage will generally involve thebalancing of the level of therapeutic benefit against any risk ordeleterious side effects of the treatments of the present invention. Theselected dosage level will depend on a variety of factors including, butnot limited to, the activity of the particular candidate tubulininhibitor, the route of administration, the time of administration, therate of excretion of the compound, the duration of the treatment, otherdrugs, compounds, and/or materials used in combination, and the age,sex, weight, condition, general health, and prior medical history of thepatient. The amount of compound and route of administration willultimately be at the discretion of the physician, although generally thedosage will be to achieve local concentrations at the site of actionwhich achieve the desired effect without causing substantial harmful ordeleterious side-effects.

Administration in vivo can be effected in one dose, continuously orintermittently (e.g. in divided doses at appropriate intervals)throughout the course of treatment. Methods of determining the mosteffective means and dosage of administration are well known to those ofskill in the art and will vary with the formulation used for therapy,the purpose of the therapy, the target cell being treated, and thesubject being treated. Single or multiple administrations can be carriedout with the dose level and pattern being selected by the treatingphysician.

Some of the examples of diseases treatable by candidate tubulininhibitors of the present invention are disclosed herein but they arenot in any way limiting to the scope of the present invention.

Examples of Various Diseases

Various diseases that can be treated by the candidate tubulin inhibitorsof the present invention include, but are not limited to, cancer typesincluding adrenal cortical cancer, anal cancer, aplastic anemia, bileduct cancer, bladder cancer, bone cancer, bone metastasis, adult CNSbrain tumors, children CNS brain tumors, breast cancer, castlemandisease, cervical cancer, childhood Non-Hodgkin's lymphoma, colon andrectum cancer, endometrial cancer, esophagus cancer, Ewing's family oftumors, eye cancer, gallbladder cancer, gastrointestianl carcinoidtumors, gastrointestinal stromal tumors, gestational trophoblasticdisease, Hodgkin's disease, Kaposi'sarcoma, kidney cancer, laryngeal andhypopharyngeal cancer, acute lymphocytic leukemia, acute myeloidleukemia, children's leukemia, chronic lymphocytic leukemia, chronicmyeloid leukemia, liver cancer, lung cancer, lung carcinoid tumors,Non-Hodgkin's lymphoma, male breast cancer, malignant mesothelioma,multiple myeloma, myelodysplastic syndrome, nasal cavity and paranasalcancer, nasopharyngeal cancer, neuroblastoma, oral cavity andoropharyngeal cancer, osteosarcoma, ovarian cancer, pancreatic cancer,penile cancer, pituitary tumor, prostate cancer, retinoblastoma,rhabdomyosarcoma, salivary gland cancer, sarcoma (adult soft tissuecancer), melanoma skin cancer, nonmelanoma skin cancer, stomach cancer,testicular cancer, thymus cancer, thyroid cancer, uterine sacrcoma,vaginal cancer, vulvar cancer, Waldenstrom's macroglobulinemia, chroniclymphocyte leukemia, and reactive lymphoid hyperplasia.

The diseases include cancer angiogenesis, new or establishedvascularization of tumors, and tumor cell proliferation and metastasis.Certain of the compounds described herein are also useful in thepromotion of angiogenesis, thus one embodiment of the present inventionis to treat diseases requiring growth of new blood vessels. Suchdiseases include, but are not limited to, myocardial hypertrophy,angina, and high blood pressure. The invention in an embodiment alsoprovides methods to treat other diseases, such as, metabolic diseaseslike gout.

Examples of Cancer

The cancer include but are not limited to, adrenal cortical cancer, analcancer, aplastic anemia, bile duct cancer, bladder cancer, bone cancer,bone metastasis, Adult CNS brain tumors, Children CNS brain tumors,breast cancer, blood cancer, Castleman Disease, cervical cancer,Childhood Non-Hodgkin's lymphoma, colon and rectum cancer, endometrialcancer, esophagus cancer, Ewing's family of tumors, eye cancer,gallbladder cancer, gastrointestianl carcinoid tumors, gastrointestinalstromal tumors, gestational trophoblastic disease, Hodgkin's disease,Kaposi'sarcoma, kidney cancer, laryngeal and hypopharyngeal cancer,acute lymphocytic leukemia, acute myeloid leukemia; children's leukemia,chronic lymphocytic leukemia, chronic myeloid leukemia, liver cancer,lung cancer, lung carcinoid tumors, Non-Hodgkin's lymphoma, male breastcancer, malignant mesotheliorna, multiple myeloma, myelodysplasticsyndrome, nasal cavity and paranasal cancer, nasopharyngeal cancer,neuroblastoma, oral cavity and oropharyngeal cancer, osteosarcoma,ovarian cancer, pancreatic cancer, penile cancer, pituitary tumor,prostate cancer, retinoblastoma, rhabdomyosarcoma, salivary glandcancer, sarcoma (adult soft tissue cancer), melanoma skin cancer,nonmelanoma skin cancer, stomach cancer, testicular cancer, thymuscancer, thyroid cancer, uterine sacrcoma, vaginal cancer, vulvar cancer,and Waldenstrom's macroglobulinemia.

Carcinoma of the thyroid gland is the most common malignancy of theendocrine system. Carcinoma of the thyroid gland include differentiatedtumors (papillary or follicular) and poorly differentiated tumors(medullary or anaplastic). Carcinomas of the vagina include squamouscell carcinoma, adenocarcinoma, melanoma and sarcoma. Testicular canceris broadly divided into seminoma and nonseminoma types.

Thymomas are epithelial tumors of the thymus, which may or may not beextensively infiltrated by non-neoplastic lymphocytes. The term thymomais customarily used to describe neoplasms that show no overt atypia ofthe epithelial component. A thymic epithelial tumor that exhibitsclear-cut cytologic atypia and histologic features no longer specific tothe thymus is known as a thymic carcinoma (also known as type Cthymoma).

The methods provided by the invention can comprise the administration ofthe tubulin inhibitor sin combination with other therapies. The choiceof therapy that can be co-administered with the compositions of theinvention can depend, in part, on the condition being treated. Forexample, for treating acute myleoid leukemia, a tubulin inhibitor can beused in combination with radiation therapy, monoclonal antibody therapy,chemotherapy, bone marrow transplantation, gene therapy, immunotherapy,or a combination thereof.

Her-2 Related Cancer

Her-2 disease is a type of breast cancer. Characterized by aggressivegrowth and a poor prognosis, it can be caused by the presence ofexcessive numbers of a gene called HER2 (human epidermal growth factorreceptor-2) in tumor cells. Therapies that can used in combination withthe tubulin inhibitor s as disclosed herein include, but are no limitedto Her-2 antibodies such as herceptin, anti-hormones (e.g., selectiveoestrogen receptor modulator (SERM) tamoxifen), chemotherapy andradiotherapy, aromatase inhibitors (e.g. anastrazole, letrozole andexemestane) and anti-oestrogens (e.g., fulvestrant (Faslodex)).

Blood Cancer

Lymphoma

B-Cell Lymphomas

Non-Hodgkin's Lymphomas caused by malignant (cancerous) B-Celllymphocytes represent a large subset (about 85% in the US) of the knowntypes of lymphoma (the other 2 subsets being T-Cell lymphomas andlymphomas where the cell type is the Natural Killer Cell or unknown).Cells undergo many changes in their life cycle dependent on complexsignaling processes between cells and interaction with foreignsubstances in the body. Apparently various types of lymphoma or leukemiacan occur in the B-Cell life cycle.

Breast Cancer

A lobular carcinoma in situ and a ductal carcinoma in situ are breastcancers that develop in the lobules and ducts, respectively, but may nothave spread to the fatty tissue surrounding the breast or to other areasof the body. An infiltrating (or invasive) lobular and a ductalcarcinoma are cancers that have developed in the lobules and ducts,respectively, and have spread to either the breast's fatty tissue and/orother parts of the body. Other cancers of the breast that can benefitfrom treatment provided by the methods of the present invention aremedullary carcinomas, colloid carcinomas, tubular carcinomas, andinflammatory breast cancer.

In some embodiments, the invention provides for treatment of so-called“triple negative” breast cancer. There are several subclasses of breastcancer identified by classic biomarkers such as estrogen receptor (ER)and/or progesterone receptor (PR) positive tumors, HER2-amplifiedtumors, and ER/PR/HER2-negative tumors. These three subtypes have beenreproducibly identified by gene expression profiling in multiple breastcancer and exhibit basal-like subtype expression profiles and poorprognosis. Triple negative breast cancer is characterized byER/PR/HER2-negative tumors.

Ovarian Cancer

The ovarian cancer includes but is not limited to, epithelial ovariantumors, adenocarcinoma in the ovary and an adenocarcinoma that hasmigrated from the ovary into the abdominal cavity. Treatments forovarian cancer that can be used in combination with the tubulininhibitors of the present invention include but are not limited to,surgery, immunotherapy, chemotherapy, hormone therapy, radiationtherapy, or a combination thereof. Some possible surgical proceduresinclude debulking, and a unilateral or bilateral oophorectomy and/or aunilateral or bilateral salpigectomy.

Anti-cancer drugs that can be used in the combination therapy includecyclophosphamide, etoposide, altretamine, and ifosfamide. Hormonetherapy with the drug tamoxifen can be used to shrink ovarian tumors.Radiation therapy can be external beam radiation therapy and/orbrachytherapy.

Cervical Cancer

The cervical cancer includes, but is not limited to, an adenocarcinomain the cervix epithelial. Two main types of this cancer exist: squamouscell carcinoma and adenocarcinomas. Some cervical cancers havecharacteristics of both of these and are called adenosquamous carcinomasor mixed carcinomas.

Prostate Cancer

The prostate cancer includes, but is not limited to, an adenocarcinomaor an adenocarinoma that has migrated to the bone. Prostate cancerdevelops in the prostate organ in men, which surrounds the first part ofthe urethra.

Pancreatic Cancer

The pancreatic cancer includes, but is not limited to, an epitheliodcarcinoma in the pancreatic duct tissue and an adenocarcinoma in apancreatic duct. Treatments that can be used in combination with thetubulin inhibitor s of the present invention include but are not limitedto, surgery, immunotherapy, radiation therapy, and chemotherapy.Possible surgical treatment options include a distal or totalpancreatectomy and a pancreaticoduodenectomy (Whipple procedure).Radiation therapy can be an option for pancreatic cancer patients, suchas external beam radiation where radiation is focused on the tumor by amachine outside the body. Another option is intraoperative electron beamradiation administered during an operation.

Bladder Cancer

The bladder cancer includes, but is not limited to, a transitional cellcarcinoma in urinary bladder. Bladder cancers are urothelial carcinomas(transitional cell carcinomas) or tumors in the urothelial cells thatline the bladder. The remaining cases of bladder cancer are squamouscell carcinomas, adenocarcinomas, and small cell cancers. Severalsubtypes of urothelial carcinomas exist depending on whether they arenoninvasive or invasive and whether they are papillary, or flat.Noninvasive tumors are in the urothelium, the innermost layer of thebladder, while invasive tumors have spread from the urothelium to deeperlayers of the bladder's main muscle wall. Invasive papillary urothelialcarcinomas are slender finger-like projections that branch into thehollow center of the bladder and also grow outward into the bladderwall. Non-invasive papillary urothelial tumors grow towards the centerof the bladder. While a non-invasive, flat urothelial tumor (also calleda flat carcinoma in situ) is confined to the layer of cells closest tothe inside hollow part of the bladder, an invasive flat urothelialcarcinoma invades the deeper layer of the bladder, particularly themuscle layer.

The therapies that can be used in combination with the tubulininhibitors of the present invention for the treatment of bladder cancerinclude surgery, radiation therapy, immunotherapy, chemotherapy, or acombination thereof. Some surgical options are a transurethralresection, a cystectomy, or a radical cystectomy. Radiation therapy forbladder cancer can include external beam radiation and brachytherapy.

Immunotherapy is another method that can be used to treat a bladdercancer patient. One method is Bacillus Calmete-Guerin (BCG) where abacterium sometimes used in tuberculosis vaccination is given directlyto the bladder through a catheter. The body mounts an immune response tothe bacterium, thereby attacking and killing the cancer cells. Anothermethod of immunotherapy is the administration of interferons,glycoproteins that modulate the immune response. Interferon alpha isoften used to treat bladder cancer.

Anti-cancer drugs that can be used in combination to treat bladdercancer include thitepa, methotrexate, vinblastine, doxorubicin,cyclophosphamide, paclitaxel, carboplatin, cisplatin, ifosfamide,gemcitabine, or combinations thereof.

Acute Myeloid Leukemia

The acute myeloid leukemia (AML) includes acute promyleocytic leukemiain peripheral blood. AML begins in the bone marrow but can spread toother parts of the body including the lymph nodes, liver, spleen,central nervous system, and testes. AML can be characterized by immaturebone marrow cells usually granulocytes or monocytes, which can continueto reproduce and accumulate.

AML can be treated by other therapies in combination with the tubulininhibitors of the present invention. Such therapies include but are notlimited to, immunotherapy, radiation therapy, chemotherapy, bone marrowor peripheral blood stem cell transplantation, or a combination thereof.Radiation therapy includes external beam radiation and can have sideeffects. Anti-cancer drugs that can be used in chemotherapy to treat AMLinclude cytarabine, anthracycline, anthracenedione, idarubicin,daunorubicin, idarubicin, mitoxantrone, thioguanine, vincristine,prednisone, etoposide, or a combination thereof.

Monoclonal antibody therapy can be used to treat AML patients. Smallmolecules or radioactive chemicals can be attached to these antibodiesbefore administration to a patient in order to provide a means ofkilling leukemia cells in the body. The monoclonal antibody, gemtuzumabozogamicin, which binds CD33 on AML cells, can be used to treat AMLpatients unable to tolerate prior chemotherapy regimens. Bone marrow orperipheral blood stem cell transplantation can be used to treat AMLpatients. Some possible transplantation procedures are an allogenic oran autologous transplant.

Other types of leukemia's that can be treated by the methods provided bythe invention include but not limited to, Acute Lymphocytic Leukemia,Chronic Lymphocytic Leukemia, Chronic Myeloid Leukemia, Hairy CellLeukemia, Myelodysplasia, and Myeloproliferative Disorders.

Lung Cancer

The common type of lung cancer is non-small cell lung cancer (NSCLC),which is divided into squamous cell carcinomas, adenocarcinomas, andlarge cell undifferentiated carcinomas. Treatment options for lungcancer in combination with the tubulin inhibitors of the presentinvention include surgery, immunotherapy, radiation therapy,chemotherapy, photodynamic therapy, or a combination thereof. Somepossible surgical options for treatment of lung cancer are a segmentalor wedge resection, a lobectomy, or a pneumonectomy. Radiation therapycan be external beam radiation therapy or brachytherapy.

Some anti-cancer drugs that can be used in chemotherapy to treat lungcancer include cisplatin, carboplatin, paclitaxel, docetaxel,gemcitabine, vinorelbine, irinotecan, etoposde, vinblastine, gefitinib,ifosfamide, methotrexate, or a combination thereof. Photodynamic therapy(PDT) can be used to treat lung cancer patients.

Skin Cancer

There are several types of cancer that start in the skin. The mostcommon types are basal cell carcinoma and squamous cell carcinoma, whichare non-melanoma skin cancers. Actinic keratosis is a skin conditionthat sometimes develops into squamous cell carcinoma. Non-melanoma skincancers rarely spread to other parts of the body. Melanoma, the rarestform of skin cancer, is more likely to invade nearby tissues and spreadto other parts of the body.

Different types of treatments that can be used in combination with thetubulin inhibitors of the present invention include but are not limitedto, surgery, radiation therapy, chemotherapy and photodynamic therapy.Some possible surgical options for treatment of skin cancer are mohsmicrographic surgery, simple excision, electrodesiccation and curettage,cryosurgery, laser surgery. Radiation therapy can be external beamradiation therapy or brachytherapy. Other types of treatments includebiologic therapy or immunotherapy, chemoimmunotherapy, topicalchemotherapy with fluorouracil and photodynamic therapy.

Eye Cancer, Retinoblastoma

Retinoblastoma is a malignant tumor of the retina. The tumor can be inone eye only or in both eyes. Treatment options that can be used incombination with the tubulin inhibitors of the present invention includeenucleation (surgery to remove the eye), radiation therapy, cryotherapy,photocoagulation, immunotherapy, thermotherapy and chemotherapy.Radiation therapy can be external beam radiation therapy orbrachytherapy.

Eye Cancer, Intraocular Melanoma

Intraocular melanoma is a disease in which cancer cells are found in thepart of the eye called the uvea. The uvea includes the iris, the ciliarybody, and the choroid. Intraocular melanoma occurs most often in peoplewho are middle aged. Treatments that can be used in combination with thetubulin inhibitors of the present invention include surgery,immunotherapy, radiation therapy and laser therapy. Surgery is the mostcommon treatment of intraocular melanoma. Some possible surgical optionsare iridectomy, iridotrabeculectomy, iridocyclectomy, choroidectomy,enucleation and orbital exenteration. Radiation therapy can be externalbeam radiation therapy or brachytherapy. Laser therapy can be anintensely powerful beam of light to destroy the tumor, thermotherapy orphotocoagulation.

Endometrium Cancer

Endometrial cancer is a cancer that starts in the endometrium, the innerlining of the uterus. Some of the examples of the cancer of uterus andendometrium include, but are not limited to, adenocarcinomas,adenoacanthomas, adenosquamous carcinomas, papillary serousadenocarcinomas, clear cell adenocarcinomas, uterine sarcomas, stromalsarcomas, malignant mixed mesodermal tumors, and leiomyosarcomas.

Liver Cancer

Primary liver cancer can occur in both adults and children. Differenttypes of treatments that can be used in combination with the tubulininhibitors of the present invention include surgery, immunotherapy,radiation therapy, chemotherapy and percutaneous ethanol injection. Thetypes of surgery that can be used are cryosurgery, partial hepatectomy,total hepatectomy and radiofrequency ablation. Radiation therapy can beexternal beam radiation therapy, brachytherapy, radiosensitizers orradioiabel antibodies. Other types of treatment include hyperthermiatherapy and immunotherapy.

Kidney Cancer

Kidney cancer (also called renal cell cancer or renal adenocarcinoma) isa disease in which malignant cells are found in the lining of tubules inthe kidney. Treatments that can be used in combination with the tubulininhibitors of the present invention include surgery, radiation therapy,chemotherapy and immunotherapy. Some possible surgical options to treatkidney cancer are partial nephrectomy, simple nephrectomy and radicalnephrectomy. Radiation therapy can be external beam radiation therapy orbrachytherapy. Stem cell transplant can be used to treat kidney cancer.

Thyroid Cancer

Thyroid cancer is a disease in which cancer (malignant) cells are foundin the tissues of the thyroid gland. The four main types of thyroidcancer are papillary, follicular, medullary and anaplastic. Thyroidcancer can be treated by surgery, immunotherapy, radiation therapy,hormone therapy and chemotherapy. Some possible surgical options thatcan be used in combination with the tubulin inhibitors of the presentinvention include but are not limited to, lobectomy, near-totalthyroidectomy, total thyroidectomy and lymph node dissection. Radiationtherapy can be external radiation therapy or can require intake of aliquid that contains radioactive iodine. Hormone therapy uses hormonesto stop cancer cells from growing. In treating thyroid cancer, hormonescan be used to stop the body from making other hormones that might makecancer cells grow.

AIDS-Related Lymphoma

AIDS-related lymphoma is a disease in which malignant cells form in thelymph system of patients who have acquired immunodeficiency syndrome(AIDS). AIDS is caused by the human immunodeficiency virus (HIV), whichattacks and weakens the body's immune system. The immune system is thenunable to fight infection and diseases that invade the body. People withHIV disease have an increased risk of developing infections, lymphoma,and other types of cancer. Lymphomas are cancers that affect the whiteblood cells of the lymph system. Lymphomas are divided into two generaltypes: Hodgkin's lymphoma and non-Hodgkin's lymphoma. Both Hodgkin'slymphoma and non-Hodgkin's lymphoma can occur in AIDS patients, butnon-Hodgkin's lymphoma is more common. When a person with AIDS hasnon-Hodgkin's lymphoma, it is called an AIDS-related lymphoma.Non-Hodgkin's lymphomas can be indolent (slow-growing) or aggressive(fast-growing). AIDS-related lymphoma is usually aggressive. The threemain types of AIDS-related lymphoma are diffuse large B-cell lymphoma,B-cell immunoblastic lymphoma and small non-cleaved cell lymphoma.

Highly-active antiretroviral therapy (HAART) is used to slow progressionof HIV. Medicine to prevent and treat infections, which can be serious,is also used. AIDS-related lymphomas can be treated by chemotherapy,immunotherapy, radiation therapy and high-dose chemotherapy with stemcell transplant. Radiation therapy can be external beam radiationtherapy or brachytherapy. AIDS-related lymphomas can be treated bymonoclonal antibody therapy.

Kaposi's Sarcoma

Kaposi's sarcoma is a disease in which cancer cells are found in thetissues under the skin or mucous membranes that line the mouth, nose,and anus. Kaposi's sarcoma can occur in people who are takingimmunosuppressants. Kaposi's sarcoma in patients who have AcquiredImmunodeficiency Syndrome (AIDS) is called epidemic Kaposi's sarcoma.Kaposi's sarcoma can be treated with surgery, chemotherapy, radiationtherapy and immunotherapy. External radiation therapy is a commontreatment of Kaposi's sarcoma. Treatments that can be used incombination with the tubulin inhibitors of the present invention includebut are not limited to, local excision, electrodeiccation and curettage,and cryltherapy.

Viral-Induced Cancers

The virus-malignancy systems include hepatitis B virus (HBV), hepatitisC virus (HCV), and hepatocellular carcinoma; human lymphotropicvirus-type 1 (HTLV-1) and adult T-cell leukemia/lymphoma; and humanpapilloma virus (HPV) and cervical cancer.

Virus-Induced Hepatocellular Carcinoma

HBV and HCV and hepatocellular carcinoma or liver cancer can appear toact via chronic replication in the liver by causing cell death andsubsequent regeneration. Treatments that can be used in combination withthe tubulin inhibitors of the present invention include but are notlimited to, include surgery, immunotherapy, radiation therapy,chemotherapy and percutaneous ethanol injection. The types of surgerythat can be used are cryosurgery, partial hepatectomy, total hepatectomyand radiofrequency ablation. Radiation therapy can be external beamradiation therapy, brachytherapy, radiosensitizers or radiolabelantibodies. Other types of treatment include hyperthermia therapy andimmunotherapy.

Viral-Induced Adult T Cell Leukemia/Lymphoma

Adult T cell leukemia is a cancer of the blood and bone marrow. Thetreatments for adult T cell leukemia/lymphoma that can be used incombination with the tubulin inhibitors of the present invention includebut are not limited to, radiation therapy, immunotherapy, andchemotherapy. Radiation therapy can be external beam radiation therapyor brachytherapy. Other methods of treating adult T cellleukemia/lymphoma include immunotherapy and high-dose chemotherapy withstem cell transplantion.

Viral-Induced Cervical Cancer

Infection of the cervix with human papillomavirus (HPV) is a cause ofcervical cancer. The treatments for cervical cancers that can be used incombination with the tubulin inhibitors of the present invention includebut are not limited to, surgery, immunotherapy, radiation therapy andchemotherapy. The types of surgery that can be used are conization,total hysterectomy, bilateral salpingo-oophorectomy, radicalhysterectomy, pelvic exenteration, cryosurgery, laser surgery and loopelectrosurgical excision procedure. Radiation therapy can be externalbeam radiation therapy or brachytherapy.

CNS Cancers

Brain and spinal cord tumors are abnormal growths of tissue found insidethe skull or the bony spinal column, which are the primary components ofthe central nervous system (CNS). Benign tumors are non-cancerous, andmalignant tumors are cancerous. Tumors that originate in the brain orspinal cord are called primary tumors. Primary tumors can result fromspecific genetic disease (e.g., neurofibromatosis, tuberous sclerosis)or from exposure to radiation or cancer-causing chemicals.

The primary brain tumor in adults comes from cells in the brain calledastrocytes that make up the blood-brain barrier and contribute to thenutrition of the central nervous system. These tumors are called gliomas(astrocytoma, anaplastic astrocytoma, or glioblastoma multiforme). Someof the tumors are, but not limited to, Oligodendroglioma, Ependymoma,Meningioma, Lymphoma, Schwannoma, and Medulloblastoma.

Neuroepithelial Tumors of the CNS

Astrocytic tumors, such as astrocytoma; anaplastic (malignant)astrocytoma, such as hemispheric, diencephalic, optic, brain stem,cerebellar; glioblastoma multiforme; pilocytic astrocytoma, such ashemispheric, diencephalic, optic, brain stem, cerebellar; subependymalgiant cell astrocytoma; and pleomorphic xanthoastrocytoma.Oligodendroglial tumors, such as oligodendroglioma; and anaplastic(malignant) oligodendroglioma. Ependymal cell tumors, such asependymoma; anaplastic ependymoma; myxopapillary ependymoma; andsubependymoma. Mixed gliomas, such as mixed oligoastrocytoma; anaplastic(malignant) oligoastrocytoma; and others (e.g. ependymo-astrocytomas).Neuroepithelial tumors of uncertain origin, such as polarspongioblastoma; astroblastoma; and gliomatosis cerebri. Tumors of thechoroid plexus, such as choroid plexus papilloma; and choroid plexuscarcinoma (anaplastic choroid plexus papilloma). Neuronal and mixedneuronal-glial tumors, such as gangliocytoma; dysplastic gangliocytomaof cerebellum (Lhermitte-Duclos); ganglioglioma; anaplastic (malignant)ganglioglioma; desmoplastic infantile ganglioglioma, such asdesmoplastic infantile astrocytoma; central neurocytoma;dysembryoplastic neuroepithelial tumor; olfactory neuroblastoma(esthesioneuroblastoma. Pineal Parenchyma Tumors, such as pineocytoma;pineoblastoma; and mixed pineocytoma/pineoblastoma. Tumors withneuroblastic or glioblastic elements (embryonal tumors), such asmedulloepithelioma; primitive neuroectodermal tumors with multipotentdifferentiation, such as medulloblastoma; cerebral primitiveneuroectodermal tumor; neuroblastoma; retinoblastoma; andependymoblastoma.

Other CNS Neoplasms

Tumors of the sellar region, such as pituitary adenoma; pituitarycarcinoma; and craniopharyngioma. Hematopoietic tumors, such as primarymalignant lymphomas; plasmacytoma; and granulocytic sarcoma. Germ CellTumors, such as germinoma; embryonal carcinoma; yolk sac tumor(endodermal sinus tumor); choriocarcinoma; teratoma; and mixed germ celltumors. Tumors of the Meninges, such as meningioma; atypical meningioma;and anaplastic (malignant) meningioma. Non-menigothelial tumors of themeninges, such as Benign Mesenchymal; Malignant Mesenchymal; PrimaryMelanocytic Lesions; Hemopoietic Neoplasms; and Tumors of UncertainHistogenesis, such as hemangioblastoma (capillary hemangioblastoma).Tumors of Cranial and Spinal Nerves, such as schwannoma (neurinoma,neurilemoma); neurofibroma; malignant peripheral nerve sheath tumor(malignant schwannoma), such as epithelioid, divergent mesenchymal orepithelial differentiation, and melanotic. Local Extensions fromRegional Tumors; such as paraganglioma (chemodectoma); chordoma;chodroma; chondrosarcoma; and carcinoma. Metastatic tumours,Unclassified Tumors and Cysts and Tumor-like Lesions, such as Rathkecleft cyst; Epidermoid; dermoid; colloid cyst of the third ventricle;enterogenous cyst; neuroglial cyst; granular cell tumor (choristoma,pituicytoma); hypothalamic neuronal hamartoma; nasal glial herterotopia;and plasma cell granuloma.

Chemotherapeutics available are, but not limited to, alkylating agentssuch as, Cyclophosphamide, Ifosphamide, Melphalan, Chlorambucil, BCNU,CCNU, Decarbazine, Procarbazine, Busulfan, and Thiotepa; antimetabolitessuch as, Methotraxate, 5-Fluorouracil, Cytarabine, Gemcitabine(Gemzar®), 6-mercaptopurine, 6-thioguanine, Fludarabine, and Cladribine;anthracyclins such as, daunorubicin. Doxorubicin, Idarubicin, Epirubicinand Mitoxantrone; antibiotics such as, Bleomycin; camptothecins such as,irinotecan and topotecan; taxanes such as, paclitaxel and docetaxel; andplatinums such as, Cisplatin, carboplatin, and Oxaliplatin.

PNS Cancers

The peripheral nervous system consists of the nerves that branch outfrom the brain and spinal cord. These nerves form the communicationnetwork between the CNS and the body parts. The peripheral nervoussystem is further subdivided into the somatic nervous system and theautonomic nervous system. The somatic nervous system consists of nervesthat go to the skin and muscles and is involved in conscious activities.The autonomic nervous system consists of nerves that connect the CNS tothe visceral organs such as the heart, stomach, and intestines. Itmediates unconscious activities.

Acoustic neuromas are benign fibrous growths that arise from the balancenerve, also called the eighth cranial nerve or vestibulocochlear nerve.The malignant peripheral nerve sheath tumor (MPNST) is the malignantcounterpart to benign soft tissue tumors such as neurofibromas andschwannomas. It is most common in the deep soft tissue, usually in closeproximity of a nerve trunk. The most common sites include the sciaticnerve, brachial plexus, and sarcal plexus.

The MPNST can be classified into three major categories withepithelioid, mesenchymal or glandular characteristics. Some of the MPNSTinclude but not limited to, subcutaneous malignant epithelioidschwannoma with cartilaginous differentiation, glandular malignantschwannoma, malignant peripheral nerve sheath tumor with perineurialdifferentiation, cutaneous epithelioid malignant nerve sheath tumor withrhabdoid features, superficial epithelioid MPNST, triton Tumor (MPNSTwith rhabdomyoblastic differentiation), schwannoma with rhabdomyoblasticdifferentiation. Rare MPNST cases contain multiple sarcomatous tissuetypes, especially osteosarcoma, chondrosarcoma and angiosarcoma. Thesehave sometimes been indistinguishable from the malignant mesenchymoma ofsoft tissue.

Other types of PNS cancers include but not limited to, malignant fibrouscytoma, malignant fibrous histiocytoma, malignant meningioma, malignantmesothelioma, and malignant mixed Müllerian tumor.

Oral Cavity and Oropharyngeal Cancer

Cancers of the oral cavity include but are not limited to,hypopharyngeal cancer, laryngeal cancer, nasopharyngeal cancer, andoropharyngeal cancer.

Stomach Cancer

There are three main types of stomach cancers: lymphomas, gastricstromal tumors, and carcinoid tumors. Lymphomas are cancers of theimmune system tissue that are sometimes found in the wall of thestomach. Gastric stromal tumors develop from the tissue of the stomachwall. Carcinoid tumors are tumors of hormone-producing cells of thestomach.

Testicular Cancer

Testicular cancer is cancer that typically develops in one or bothtesticles in young men. Cancers of the testicle develop in certain cellsknown as germ cells. The two types of germ cell tumors (GCTs) that occurin men are seminomas (60%) and non-seminomas (40%). Tumors can alsoarise in the supportive and hormone-producing tissues, or stroma, of thetesticles. Such tumors are known as gonadal stromal tumors. The twotypes are Leydig cell tumors and Sertoli cell tumors. Secondarytesticular tumors are those that start in another organ and then spreadto the testicle. Lymphoma is a secondary testicular cancer.

Thymus Cancer

The thymus is a small organ located in the upper/front portion of yourchest, extending from the base of the throat to the front of the heart.The thymus contains two main types of cells, thymic epithelial cells andlymphocytes. Thymic epithelial cells can give origin to thymomas andthymic carcinomas. Lymphocytes, whether in the thymus or in the lymphnodes, can become malignant and develop into cancers called Hodgkindisease and non-Hodgkin lymphomas. The thymus cancer includes Kulchitskycells, or neuroendocrine cells, which normally release certain hormones.These cells can give rise to cancers, called carcinoids or carcinoidtumors.

Treatments that can be used in combination with the tubulin inhibitorsof the present invention include but are not limited to, surgery,immunotherapy, chemotherapy, radiation therapy, combination ofchemotherapy and radiation therapy or biological therapy. Anticancerdrugs that have been used in the treatment of thymomas and thymiccarcinomas are doxorubicin (Adriamycin), cisplatin, ifosfamide, andcorticosteroids (prednisone).

EXAMPLES Synthetic Examples Synthetic Example 1 Synthesis of1-(4-(3-amino-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone (Formula IIIB)

The synthesis of1-(4-(3-amino-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone, representedby formula IIIB, was carried out as follows:

The compound of formula IIIB was synthesized from1-(3,5-diiodo-4-(4-methoxyphenoxy)phenyl)ethanone (DIPE) according tothe following procedure: The synthesis of DIPE has been previouslydescribed, e.g. in U.S. Pat. No. 5,922,775, U.S. Pat. No. 6,303,629,U.S. Pat. No. 5,908,861 and U.S. Pat. No. 6,326,402.

Nitration of DIPE to form1-(3,5-diiodo-4-(4-methoxy-3-nitrophenoxy)phenyl)ethanone

Nitration of DIPE was performed with a mixture of 1.4 equiv. 69% nitricacid and 2.2 equiv. 96% sulfuric acid at Ti <5° C. in methylenechloride. The reaction was complete after 30 min. According to TLC asingle product was formed, indicating that mono-nitration took place.The product isolated by extractive workup was obtained in 95% yield witha purity of 99.9 area %. As the nitro-reduced product was eventuallyidentified as the compound of formula IIIB, it is inferred that theproduct of this reaction is1-(3,5-diiodo-4-(4-methoxy-3-nitrophenoxy)phenyl)ethanone (3-nitrointermediate).

Reduction of Nitro Group to Form the Compound of Formula IIIB

The reduction of the nitro group was carried out with 5.5 equiv. ofanhydrous tin(II) chloride in ethanol, 37% HCl solution at Ti<10° C.;afterwards the solution was allowed to warm to room temperature and wasstirred at Ti=30-35° C. for 7 hours. The product was isolated as itshydrochloride salt, which was transformed into the free base uponbasification with 1N NaOH solution. An impurity at RRT=1.08 was presentin 1.9 area %. This impurity was determined to be the nitroso impurity.The crude product was re-crystallized three times from ethyl acetate.The nitroso impurity was thereby reduced to 0.4 area % and the productof formula IIIB was obtained in 99.4 area % purity as a white solid. Thestructure of formula IIIB and that of the 3-nitro intermediate weredetermined by NMR studies (¹H-, ¹³C-, HSQC-, HMBC-, NOESY- andCOSY-experiments).

Synthetic Example 2 Synthesis of1-(4-(3-hydroxy-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone (FormulaIIIA)

The synthesis of1-(4-(3-hydroxy-4-methoxyphenoxy)-3,5-diiodophenyl)ethanone, representedby formula IIIA, was carried out as follows:

Diazonium Salt Formation

A diazonium salt:

was formed by adding an aqueous solution of NaNO₂ (2.0 equiv.; c=1.4g/mL) at Ti=0-5° C. to a suspension of the compound of formula IIIB, asobtained in synthetic example 1. The reaction was followed by HPLC. Thediazonium salt is eluted at RRT of 0.78. Diazonium salt formation wascomplete within 5 hours. The conversion was 91% and the purity of thediazonium salt was 87.9 area %. Excess nitrous acid was destroyed byaddition of urea; and the reaction mixture was tested with starch iodinepaper.

Conversion of the Diazonium Salt to the Compound of Formula IIIA

The diazonium salt was added to 6N H₂SO₄ (30.6 equiv.) and the reactionmixture stirred at Ti=100° C. for 24 hours. The diazonium salt of thecompound of formula IIIB was surprisingly stable. Silica gelchromatography (methylene chloride as mobile phase) followed by normaland reverse phase chromatography resulted in 3.9 mg of compound offormula IIIA with a purity of 74.2 area % to 80.9 area %.

Example 1 Effect on Tubulin Polymerization

In the following experiments the candidate tubulin inhibitors,separately or in combination, at 1 to 5 mM concentrations inhibit theGTP-dependent polymerization of MTP as determined by an optical test.This inhibition is critically dependent on the concentration of GTP. Thequantitative correlation between the concentrations of candidate tubulininhibitors and GTP, under conditions of a linear rate of MTPpolymerization, follows Michaelis-Menten kinetics and the inhibitionportrays a “mixed” type, where km for GTP and Vmax are alteredsimultaneously. Candidate tubulin inhibitors inhibit MTP polymerizationparallel to their anti-tumorigenic action in vivo. The MTP site is oneof the early cellular response sites of the candidate tubulininhibitors.

Exposure of human mammary cancer cells (MDA-MB-231) to 1 mM of acandidate tubulin inhibitor induces abnormal spindle structures within18 hours of drug treatment, thus a putative candidate tubulininhibitor-microtubule-protein (MTP) interaction appears to be acomponent of early cellular responses to the drug. Abnormal spindlestructures could be the result of candidate tubulin inhibitor-MTPinteraction or reactions of a candidate tubulin inhibitor withcomponents of the microtubule organizing center or with as yet undefinedsystems sequentially or in concert. Since time-dependent quantitativeanalysis of the MTP system in situ is unsuitable for initial velocitymeasurement we adapted the in vitro assembly system of neurotubules as amodel for a quantitative analysis of the interaction of a candidatetubulin inhibitor with MTP. As demonstrated by Gaskin, et al., 1974,“Turbidimetric studies of the in vitro assembly and disassembly ofporcine neurotubules”, J. Mol. Biol. 89:737-758; and Kirschner, et al.,1974, “Microtubules from mammalian brain: some properties of theirdepolymerization products and a proposed mechanism of assembly anddisassembly”, Proc. Natl. Acad. Sci. U.S.A. 71:1159-1163; this system issuitable for kinetic assay of MTP assembly in vitro. The time course ofMTP assembly consists of initiation and propagation and terminationsteps, Gaskin, et al., 1974, “Turbidimetric studies of the in vitroassembly and disassembly of porcine neurotubules”, J. Mol. Biol.89:737-758. The rate of propagation under defined conditions issufficiently linear to permit kinetic analysis that can be evaluatedwith respect candidate tubulin inhibitor and GTP concentrations. As weshow here the inhibition of MTP assembly by candidate tubulin inhibitorsoccurs in the same range of drug concentration as required to inhibittumorigenesis in vivo, or to inhibit cell replication or induce eventualcell death; Mendeleyev, et al., 1997. “Structural specificity andtumoricidal action of methyl-3,5-diiodo-4-(4′-methoxyphenoxy)benzoate(DIME)” Int. J. Oncol., 10:689-695. Therefore the a candidate tubulininhibitor-MTP interaction is most probably a component of the apparentlypleiotropic cellular mechanism of action of DIME.

Isolation of Microtubule Proteins (MTP)

Preparation of MTP and an optical test for polymerization is adoptedfrom published methods, Gaskin, et al., 1974, “Turbidimetric studies ofthe in vitro assembly and disassembly of porcine neurotubules”, J. Mol.Biol. 89:737-758; Tiwari, et al., 1993, “A pH and temperature-dependentcycling method that doubles the yield of microtubule protein”, Anal.Biochem. 215:96-103. Bovine or rabbit brain is homogenized in an equalvolume of ice cold buffer containing 100 mM Pipes/K+ (pH 7.4), 4 mMEGTA. 1 mM MgCl₂, 0.5 mM DTT and 0.1 mM PMSF, and centrifuged at 39,000g for 1 hour at 4° C. To the supernatant, DMSO (8% final concentration)and GTP (1 mM final concentration) are added, followed by incubation at37° C. for 30 minutes. Microtubules are pelleted at 100,000 g at 37° C.for 30 minutes. The pellets are incubated on ice for 15 minutes,followed by resuspension in ice cold PEM buffer (100 mM Pipes/K+ (pH6.9), 1 mM EGTA, 1 mM MgCl₂). This warm polymerization and colddepolymerization cycle is repeated once more and the cold, resuspendedmonomeric MTP (8-10 mg/ml protein) is used for the optical test forpolymerization kinetics. Both rabbit or bovine brain yields identicalMTP preparations.

The polymerization reaction is started by the addition of 100 ml of MTPsolution (equivalent to 0.8-1.0 mg protein) and initial linear rates ofincrease in absorbance at 350 nm follows and is recorded at 37° C. in aPerkin-Elmer 552 double beam spectrophotometer, equipped with athermostatically controlled cuvette holder.

Inhibition of MTP polymerization can have highly complex cellularconsequences. In cytokinesis, this inhibition can interfere withtraction forces of tubulin and prevent the formation of a cleavagefurrow which is essential for cell division, Burton, et al., 1997,“Traction forces of cytokinesis measured with optically modified elasticsubstrate”, Nature 385:450-454. The inhibition of MTP polymerization bycandidate tubulin inhibitors should be correlated with the biochemicalsites of this drug.

On the basis of these experiments, it can be seen that thyroxine typeanalogues, such as the candidate tubulin inhibitors, are capable ofblocking mitosis in cancer cells.

Example 2 Anti-Tumor Efficacy of Antitubulin Inhibitors

In Vitro Cytotoxicity Screen Against Human Tumor Cell Lines.

Human tumor cell lines are exposed continuously to varyingconcentrations of test agents (i.e., candidate tubulin inhibitors) andthe viability of the cells are measured at set time points (1, 3, and 7days) using the alamar Blue™ assay. When alamar Blue™ dye is added toculture medium, the dye is reduced by cellular mitochondrial enzymesyielding a soluble product with substantially enhanced fluorescence.This fluorescence is measured with a fluorimeter, whereby the signal isdirectly proportional to cell number.

Various tumor cell lines of human origin representing a wide diversityof cancer phenotypes and genotypes are exposed in vitro to the candidatetubulin inhibitors to evaluate the drugs' effective range. Tumor linesthat are screened include MDA-MB-231 (breast), MCF-7 (breast),MDA-MB-468 (breast), Siha (squamous cell carcinoma), A549 (non-smallcell lung), HL-60 (leukemia), and Ovcar-3 (ovarian). The test agents areprepared in serial dilutions from 10 mM stock solutions in DMSO yieldinga 66-fold dose range of 20 μM, 10 μM, 3 μM, 10 μM and 0.3 μMconcentrations. In each case, cells are maintained at 37° C. in 5percent CO₂ in air. All cell lines are incubated in Dulbecco's modifiedEagle medium (DMEM) supplemented with 10% heat-inactivated fetal bovineserum and graded doses of candidate tubulin inhibitors. 5-Fluorouracil(5-FU) is included as a positive control in experiments with some thecell lines. The experiments are conducted in 96-well tissue cultureplates (Falcon) with an initial seeding density of 1000 cells per wellin 250 μL aliquots. The next day, medium is replaced with 100 μL of drugdilutions in triplicate.

After a 7 day exposure to the various agents, the alamar Blue™ dye isdiluted to 20% in DMEM, and 100 μL is added to each well. The cells areincubated for 8 hours until obvious color changes indicate sufficientamounts of reduced dye for quantitation. Relative cell number isevaluated by fluorimetry on a Millipore 2300 CytoFluor fluorescencemeasurement system. Measurements are taken directly from 96-well platesafter excitation at 560 nm with concomitant emission at 590 nm. IC50values are calculated vs. control (non-treated cells).

Example 3 In Vitro Metabolism of Candidate Tubulin Inhibitors in HumanLeukemia Cells

In humans and laboratory animals, enzyme systems in the liver arecapable of metabolizing a large number of chemicals to inactive forms,and some chemotherapeutic agents are inactive unless they aremetabolized to active forms. To test for either of these possibilities,the candidate tubulin inhibitors are incubated with a microsomal enzymefraction, referred to as S9.

Human leukemia (HL60) cells are used to evaluate drug metabolism.Exposure to the test article is performed in the presence and absence ofS9, prepared from the liver of adult male rats given a singleintraperitoneal injection of Arachlor 1254 (500 mg/kg). The S9 consistsof the 9000×G supernatant of liver homogenized in 0.25 M sucrose-100 mMphosphate buffer (pH 7.4) (Molecular Toxicology, Inc.). Cofactors are 1mM NADP and 5 mM sodium isocitrate. On the day of exposure, cultures ofcells, with or without the metabolism mixture, are incubated for 4 hoursin RPMI containing 5% FBS and graded doses of candidate tubulininhibitors. The candidate agents are prepared in serial dilutions from10 nM stock solutions in DMSO yielding a dose range 100 μM, 50 μM, 25μM, 10 μM and 5 μM concentrations and a final DMSO concentration of 1%.In each case, cells are maintained at 37° C. in 5 percent CO₂ in air.The experiments are conducted in 6-well tissue culture plates (Falcon)with an initial seeding density of 2×10⁶ cells per well in 2 mlaliquots. The test compounds are added immediately to the medium induplicate cultures. Treatment solution is removed by a series oflow-speed centrifugations to pellet the cells, followed by removal ofthe supernatant and resuspension of cells in fresh RPMI containing 10%FBS.

Example 4 In Vivo Efficacy of Candidate Tubulin Inhibitors Against Met-1Mouse Mammary Tumors

Mammary fat pads of Balb/c immunodeficient (nude) mice are implantedwith 1 mm³ of mammary tumor tissue. These mammary tumors originate fromthe met-1 mouse mammary tumor cell line and are been propagated bypassaging in vivo. When palpable tumors appear, animals are subdividedinto various treatment groups and treated daily with intraperitonealinjections of control vehicle, and candidate tubulin inhibitors (50mg/kg). A group of untreated control animals are included in the study,because agents used in the vehicle for these test articles(DMSO/ethanol/Cremophor EL/PEG 400, 1:0.5:0.5:6) are themselves found tohave cytotoxic activity. Twice weekly, the volumes of the tumors in eachanimal in each group are measured to gather information on tumor growth(volume) as a function of type of treatment, dose, and time.

Example 5 Anti-Angiogenic Properties: the Chick Chorioallantoic Membrane(CAM) Assay

Candidate tubulin inhibitors are tested in the CAM assay. The endpointof the CAM assay is a quantitative determination of basement membranebiosynthesis by measuring the incorporation of ¹⁴C-proline into Type IVcollagenous protein.

The CAM assay involves the development of live chick embryos in Petridishes under special sterile conditions. Therefore, only limited numbersof embryos can be used for evaluation of compounds in a singleexperiment. Candidate tubulin inhibitors are tested in separate assays.A known angiogenesis inhibitor, 2-methoxyestradiol (2-ME), is used asthe positive control, and human fibroblast growth factor (hFGF) is usedto induce angiogenesis in the CAM.

Fertilized eggs are supplied by Melody. Ranch, Aptos, Calif. L-[U-¹⁴C]proline (specific activity, 290 mCi/mmol) is purchased from New EnglandNuclear, Boston, Mass. Collagenase and 2-ME were obtained from SigmaChemical Co., St. Louis, Mo. Silicone ring cups are obtained by cuttingsilicone tubing (3 mm diameter) into small “O” rings 1 mm in thickness.These silicone ring cups can be reused many times if they are sterilizedprior to each assay. Plastic Petri dishes (20×100 mm) are purchase fromBaxter diagnostics, Inc., Hayward, Calif. hFGF-B is obtained fromClonetics Corporation, San Diego, Calif.

For testing, a minimum amount of acetone-methanol (1:1) is added to thetest compounds for sterilization. The acetone-methanol mixture is thenevaporated to dryness in a sterile hood. The compounds are dissolved indimethyl sulfoxide (DMSO) first and subsequently diluted with salinecontaining methylcellulose. The final concentrations are 2% DMSO and0.5% methylcellulose. All test solutions are added to each CAM in 20-mlaliquots.

The method of Folkman, et al. (Folkman, et al. (1974) Dev. Biol.41:391-394) with some modifications, is used to cultivate chickenembryos as follows:

Fresh fertile eggs are incubated for three days in a standard eggincubator. On Day 3, eggs are cracked under sterile conditions andembryos are placed in 20×100 mm plastic Petri dishes and cultivated at37° C. in an embryo incubator with a water reservoir on the bottomshelf. Air is continuously bubbled into the water reservoir by using asmall pump so that the humidity in the incubator is kept constant.Observations are made daily to ensure that all embryos are healthy. Deador unhealthy embryos are removed from the incubator immediately to avoidcontamination. On Day 9, a sterile silicone ring cup is placed on eachCAM and 0.5 mCi of ¹⁴C-proline with or without the test compound plus2.5 ng of hFGF dissolved in saline containing 0.5% methylcellulose isdelivered into each ring cup in a sterile hood. 2-ME id tested inparallel to serve as a reference compound. After addition of testmaterials, the embryos are returned to the incubator and cultivationcontinued. On Day 12, all embryos are transferred to a cold room at4-10° C. The anti-angiogenic effect of each test compound is determinedby using the collagenase assay to measure ¹⁴C-proline incorporation intocollagenous protein.

Example 6 Collagenase Assay for Measurement of ¹⁴C-Proline Incorporationinto Collagenous Protein

Using the procedure outlined in Maragoudakis, et al., (1989) J. PharmExp. Ther. 251:679-682, the embryos are placed on ice, and a piece ofCAM 10 mm in diameter is cut off under each ring cup and placed in aseparate tube. To each tube is added 1.0 ml of phosphate-buffered saline(PBS, pH 7.3) containing 0.11 mg cycloheximide and 0.17 mg dipyridyl.The tubes are placed in a boiling water bath for 10 min and then cooledto room temperature. The PBS in each tube is discarded aftercentrifugation at 3000×G for 10 min. The CAM residue is washed once with3 ml of 15% TCA and then three times with 3 ml of 5% TCA. Centrifugationis carried out as described above between each washing. At this pointall non-protein bound radioactivity was removed, and the CAM containingthe newly synthesized ¹⁴C-collagenous protein is suspended in 0.9 ml of0.1 N NaOH and 1.1 ml of HEPES buffer at pH 7.4. The pH of the sample isneutralized with 0.8 N HCl, using phenol red as indicator.

To digest the ¹⁴C-collagenous protein, 7.5 units of collagenase and 500mmol of calcium chloride in 40 ml of HEPES buffer is added to the abovesamples: and mixtures are incubated at 37° C. for 4 h. The reaction isstopped by adding 1.0 ml of 20% TCA containing 5 mg of tannic acid intoeach tube. After vortex mixing, the samples are centrifuged at 3000×Gfor 10 min. An aliquot of the clear supernatant was taken forscintillation counting to quantitate the radiolabeled tripeptidescorresponding to basement membrane collagen and other collagenousmaterials synthesized by the CAM from ¹⁴C-proline. The CAM pellets ineach tube are solubilized in 0.5 ml of 1.0 N NaOH by boiling in a waterbath for 5 min. An aliquot of the dissolved CAM is used for proteindetermination using the method provided by Pierce Chemical Co. Theradioactivity per milligram of protein from the CAM treated with a testcompound relative to that from the control CAM gives the percent ofangiogenesis inhibition.

Example 7 Assays Used to Screen for Anti-Mitotic Properties: MicrotubuleAssembly Inhibition Assay

A cell-free assay for measuring inhibition of the microtubule assemblycan be performed by first mixing tubulin and rhodamine-labeled tubulinat a ratio of 4:1 (Hyman, A., et al. (1990) Meth. Enzymol. 196, 478-485;Belmont, L. D., et al. (1996) Cell 84, 623-631). This tubulin solutionis then added on ice to a buffer (BRB 80; 80 mM potassium salt of PIPES(pH 7.5), 5 mM MgCl₂, 1 mM EGTA) containing 1 mM GTP and 1 mM DTr to a15 μM final concentration. Drugs at different concentrations (0.5 μl)are added to 50 μl samples of the buffered tubulin, and 10 μl of eachsolution is transferred to microfuge tubes. Each tube receives 0.4 μl ofmicrotubule seeds (Belmont, L. D., supra). Tubes are incubated at 37° C.for 10 min before adding 100 μl of BRB 80 containing 1% glutaraldehyde.Each reaction mixture (2.5 μl) is transferred to a microscope slide forfluorescence microscopy.

Microtubules in intact cells are visualized by using a mouseanti-tubulin monoclonal antibody and a fluorescein-labeled donkeyanti-mouse polyclonal antibody. Briefly, HeLa cells are plated in 2-wellchamber slides (Nunc, Napierville, Ill.) at 1.5×10⁴/ml and incubated in5% CO₂ at 37° C. for 24 h before treatment with drugs for 1 h. Afterremoving the medium, cellular microtubules are stabilized by using BRB80 containing 4 mM EGTA and 0.5% Triton X-100. The cells are fixed for 3min in methanol chilled at −20° C., washed with TBS buffer (0.15 M NaCl,0.02 M Tris-HCl, pH 7.4), and permeabilized with TBS/0.5% Triton X-100.After several washes with TBS/0.1% Triton X-100, the cells are blockedwith an antibody dilution buffer (TBS, 0.1% Triton X-100, 2% BSA, 0.1%sodium azide) for 10 min. The cells are stained in the dark with theprimary antibody for 1.5 h, and then the secondary antibody is added inthe antibody dilution buffer containing 1 μg/ml Hoechst 33342 andincubated in the dark for 45 min. The slides are mounted with n-propylgallate (2% w/v in 30% 0.1 M Tris/glycerol, pH 9.0) and sealed underglass cover slips.

Example 8 Competitive Tubulin-Binding Assay

The competitive binding of a compound to the colchicine binding site oftubulin is performed by using a spin column method (Woods, J. A., et al.(1995) British J. Cancer 71, 705-711). ¹⁴C-labeled candidate tubulininhibitor (20 μM, 10 nCi) is mixed with tubulin and colchicine atdifferent concentrations and incubated at room temperature for 1.5 h ina buffer containing 0.1 M MES (pH 6.8), 1 mM EGTA, 1 mM EDTA, and 1 mMMgCl₂. Each reaction mixture is loaded onto a column containing 1 ml ofSephadex G50 equilibrated with a buffer containing 40 mM MES (pH 7.5),40 mM Tris, and 1 mM MgSO₄. The columns are centrifuged at 900×G for 3min and the eluents are each mixed with 3 ml of CytoScint (ICN) foranalysis by liquid scintillation counting.

Example 9 Use of the Candidate Tubulin Inhibitors as Sensitizers forRadiotherapy: In Vitro Radiosensitization Assay

Radiosensitization studies are performed on cancer cells grown inculture. The test compound is added to the cells prior to, during, orafter irradiation. Radiation dosages are typically measured in units ofGy/min, with one Gy is equal to 100 rads, while one rad is the quantityof ionizing radiation that results in the absorption of 100 ergs ofenergy per gram of irradiated material. Sensitization enhancement ratios(SER) are determined at a 10% survival level. The C1.6 value (i.e., aconcentration of test compound yielding an SER of 1.6) is determined byplotting SER values against test compound concentration.

HeLa S-3 cells are grown and maintained in modified Eagles's mediumcontaining 10% fetal bovine serum in a humidity and CO₂-controlledincubator. Experimental studies are initiated on exponential culturesgrowing in 60 mm tissue culture dishes at treatment densities of 3-7×10⁵cells/dish. The doubling time of HeLa S-3 cultures is typicallyapproximately 18 hours.

A compound of formula (I) is dissolved in distilled water just prior touse and diluted 1:100 through addition of the appropriate volume tocultured cells. For ultraviolet irradiation studies, compound is addedonly during the repair period following irradiation. For X-irradiationstudies, drug is added to cultures 1 hour prior to irradiation andremains in contact with cells during irradiation.

For ultraviolet (non-ionizing) irradiation, all medium is removed fromcultures and, with the lid removed, dishes are exposed to 1.4 J/M2 ofUV254 nm light emitted from a G.E. germicidal lamp. Fresh media with orwithout test compound is then added to cultures during the subsequentrepair period. In some cases, cells are harvested immediately in orderto establish a T0 value for DNA strand breaks. X-irradiation (ionizing)of cultures is carried out in a TFI Bigshot X-ray unit at 3 mA, 50 keV,filtered with 1.5 mm Be and delivering 0.56 Gy/min to the cells (throughthe lid and 5 mls of media) as determined by a Victoreen ionizationchamber calibrated in the 10 to 50 keV range. Following X-irradiation,cultures are harvested immediately for colony forming ability assays. D0values are calculated from survival curves computer plotted by linearregression analysis.

The ability of cells to form colonies after irradiation is determined bystandard methods. Cultures treated with test compound are irradiated andimmediately trypsinized, counted and re-plated in 5 ml medium containingthe appropriate number of cells (500 for untreated cultures and culturesexposed to 2.8 Gy X-rays; 2,000 for cultures exposed to 20 J/M2 UV;5,000 for cultures exposed to 5.6 Gy X-rays and 10,000 for culturesexposed to 8.4 Gy X-rays). Cultures are grown for 10 days at which timecolonies of 1.0-2.0 mm (50-200 cells) are evaluated by methanol fixationand staining. Untreated HeLa cells exhibit cloning efficiencies in therange of 34 to 46% using this protocol.

In Vivo Radiosensitization Assay

This example describes one method by which one of skill in the art canassay the effect of the compounds of the invention on radiotherapy ofmalignant tumors. The model system used in this study is wellestablished for determining the effects of radiation on tumor tissue.See, e.g., Twentyman, et al. (1980) J. Nat'l. Cancer Inst. 64: 595-603;Brown, et al. (1980) J. Nat'l. Cancer Inst. 64: 603-611; Bernstein, etal. (1982) Radiation Res. 91: 624-637. The model uses RIF-1 tumor cells,which are well suited to studies of radiation response, including invitro cell survival and in vivo tumor studies, in part because of itsrapid growth rate, with a doubling time of 65 hours and a cell cycletime of 12 hours. The RIF-1 tumor is minimally immunogenic, andmetastasizes only at a late stage of growth.

Tumors are produced by the subcutaneous inoculation into the lower backsof mice. This inoculation consists of a suspension of 2×10⁵ RIF-1 cellsfrom culture in 0.25 ml of alpha minimum essential media (MEM, Gibso)supplemented with 10% fetal bovine serum (Johns Scientific). Male C3H/Hemice (Harlan Sprague Dawley Inc., Indianapolis, Ind.) that are 5 to 7weeks old at the time of inoculation are suitable for these experiments.Animals are anaesthetized for the inoculation.

The tumors are then allowed to grow to 1 cm in average diameter.Measurements are made using a caliper, talking the tumor length andwidth and calculating the average of these two. Tumor diametermeasurements are taken every 2 to 3 days from the time the tumor cellswere implanted.

Tumors are allowed to grow to approximately 1 cm average diameterwithout any intervention. Upon the tumors reaching this averagediameter, the subject animals are randomized into one of three groups.One group receives no radiation and no test compound, a second groupreceives radiation and no test compound and a third group receivesradiation and test compound.

For radiation treatment, each animal receives a general anesthetic.Animals immobilized and placed in the radiotherapy apparatus for thesame period of time. The radiation exposure consists of a single dose of3000 cGy of 150 KeV X-irradiation (mean time 10 minutes, 40 seconds).Preferably, the radiotherapy equipment (Protea ionization chamber) iscalibrated before and after each session to ensure absolute uniformdosing. The radiotherapy is administered with a cone over the tumor andlower back of the animal, which in every case assures a uniform maximaldelivery dose to the tumor while minimizing dose delivery to thesensitive structures of the abdomen and upper pelvis.

Those animals randomized to the test compound-treated group receive anintravenous dose of a candidate tubulin inhibitor. The day the subjectanimal is treated is designated “Day Zero”. At frequent intervals,usually every other day, the tumors are measured in the same fashion aspreviously described, and an average of two diameters calculated. Thesedata are plotted as a function of time. The end-point of the studyoccurs when the tumor reaches double the original treatment diameter, orapproximately 2 cm. Animals are euthanized in a CO₂ chamber and thetumors removed surgically post-mortem. Representative tumors aresectioned, paraffin embedded and slides are stained using H&E stain andexamined to confirm the histological presence of RIP-1 fibrosarcoma.Animals are sacrificed and tumors harvested before the tumor reachestwice the original diameter in the following situations: premature deathof animal following treatment; ulceration of the tumor; or infection orinflammation of the injection site.

Following the termination of the experiment, growth curves for eachsubject tumor are completed and a line of best fit assigned for purposesof interpolation between data points. The average diameter (AD) of eachtumor is then determined for each day of the study from the lane of bestfit.

Example 10 Use of Candidate Tubulin Inhibitors as Sensitizers forChemotherapy

Assays for determining appropriate dosages of the compounds of theinvention for use as sensitizers for chemotherapy and immunotherapy aresimilar to those described for radiotherapy. To examine the“pre-incubation effect” of the compounds of the invention, cancer cellsare exposed to a fixed concentration of a candidate tubulin inhibitortest compound for 2 hours, followed by exposure to varyingconcentrations of a chemotherapeutic or immunotherapeutic agent for 1hour at 37° C., and then assayed for colony formation. In evaluating theeffect of “pre-incubation time” on chemosensitization, cancer cells areexposed to fixed concentrations of the test compound for 0 to 4 hours at37° C., followed by exposure to a chemotherapeutic agent under aerobicconditions for 1 hour at 37° C., and then assayed for colony formation.Test compound dose-dependent potentiation also is examined by exposingcancer cells to various test compound concentrations for 2 hours at 37°C., and then to a fixed dose of each chemotherapeutic agent for 1 hourat 37° C. under aerobic conditions. Experiments using a simultaneousaddition of the sensitizer and chemotherapeutic agent for 1 hour at 37°C. under aerobic conditions can also be performed.

Example 11 Chemoprevention

The efficacy of the claimed compounds as a chemopreventive agent can bedemonstrated using in vitro and in vivo models of 5AzadC-inducedcarcinogenesis. A suitable model system uses pre-malignant murinefibroblasts (cell lines 4C8 and PR4) that express a transcriptionallyactivated c-Ha-ras protooncogene. These non-tumorigenic cells, which arehighly susceptible to malignant conversion by pharmacological doses of5AzadC, are subclones of mouse NIH 3T3 fibroblasts, PR4N and 4C8-A10(designated here PR4 and 4C8) and have been previously described (see,e.g., Wilson, et al. (1986) Anal. Biochem., 152: 275-284; Dugaiczyk(1983) Biochem. 22:1605-1613). Both cell lines are phenotypic revertantsisolated from LTR/c-Ha-ras 1-transformed 3T3 cells after long-termtreatment with murine interferon alpha/beta. Cultures are maintained inDulbecco's modified Eagle's medium (DM supplemented with 10% heatinactivated fetal calf serum (Gibco) and antibiotics. The sodium saltsof phenylacetic and phenylbutyric acids (Elan PharmaceuticalCorporation) are dissolved in distilled water. 5AzadC (Sigma St. Louis,Mo.) is dissolved in phosphate buffered saline (PBS) and stored inaliquots at −20° C. until use. Exposure of 5AzadC to direct light isavoided at all times to prevent drug hydrolysis.

For in vitro tests, cells are plated at 1-2×10⁵ cells in 100 mm dishesand the test compound added to the growth medium at 20 and 48 hrs later.The cells are subsequently subcultured and observed for phenotypicalterations. Whereas untreated 4C8 and PR4 form contact-inhibitedmonolayers composed of epithelial-like cells, transient exposure ofthese cultures to 0.1 μM 5AzadC during logarithmic phase of growthresults in rapid and massive neoplastic transformation. Within one weekof 5AzadC treatment, the great majority of the cell population becomesrefractile and spindly in shape and form multilayered cultures withincreased saturation densities, which is indicative of loss of contactinhibition of growth. Treatment of the cells with the test compoundreduces or prevents these phenotypic changes. The test compound can beadministered prior to treatment of the cells with 5AzadC, simultaneouslywith 5 AzadC treatment, or after 5AzadC treatment.

For in vivo tests of the ability of the test compounds to preventmalignancy, 6-9 week-old female athymic nude mice are inoculatedsubcutaneously (s.c.) with 0.5×10⁶ cells. Twenty four hours later 400 μgof freshly prepared 5AzadC in 200 μl PBS is administeredintraperitoneally (i.p.) into each animal (approximately 20 mg/kg). Thetest compound is also administered to the animal. The number, size, andweight of tumors is recorded after 3-4 weeks. For histologicalexamination, tumors are excised, fixed in Bouin's solution (picric acid:37% formaldehyde: glacial acetic acid, 15:5:1 vol/vol), and stained withH&E. A single i.p. injection of mice with 5AzadC (20 mg/kg) typicallyresults in tumor development at the site of 4C8 cell inoculation incontrols. However, animals protected by a compound of the inventioneither fail to develop tumors or form slow-growing lesions at the siteof 4C8 inoculation.

An additional test of the ability of the compounds of the invention toprevent malignant growth involves inhibition of cell growth on matrigel,which is a reconstituted basement membrane (Collaborative Research).This assay models the ability of cells to degrade and cross tissuebarriers. Cells are exposed for 48 hrs in plastic tissue culture disheswith 5AzadC alone or in combination with the test compound. Treatmentwith the test compound is continued for an additional 1-2 weeks, afterwhich cells are re-plated onto 16 mm dishes that were previously coatedwith 250 μl of matrigel (10 mg/ml). The test compound is either added tothe dishes or omitted in order to determine whether the effect isreversible. In the absence of test compound, net-like formationcharacteristic of invasive cells typically occurs within 12 hours, andinvasion into the matrigel is evident after 6-9 days.

Example 12 Assay for Measuring the Ability of Candidate TubulinCompounds to Reduce the Levels of Tumor Necrosis Factor (TNF-Alpha)

This example provides an assay that can be used to screen compounds ofFormula I for their ability to reduce the expression of cytokines (e.g.,TNF-alpha) in a mammal.

Cell Line

The murine macrophage PU5-1.8 cell line is purchased from the AmericanType Culture Collection (ATCC, Rockville, Md.). Cells are grown in DMEMmedium supplemented with 100 mM sodium pyruvate, 0.1 mM nonessentialamino acids, 2 mM glutamine and 5% fetal bovine serum (LifeTechnologies, Staten Island, N.Y.). Cells are maintained in a humidifiedatmosphere of 5% CO₂-95% air at 37° C. Cells are passaged twice weeklyby firmly tapping the side of the flask to dislodge the adherent cells.Both non-adherent and adherent cells are passaged. Exponentially growingcells are seeded at 5×10⁵/mL, 4 mL per 60-mm dish 24 h prior to theexperiment. Test compounds are delivered in 1 mL volumes of the mediumadded to each dish at the start of the experiment. All dishes areincubated at 37° C. in 5% CO₂-95% air for 3 h.

Reagents.

The Tumor Necrosis Factor (TNF-alpha) cDNA is obtained from the ATCC(Rockville, Md.). [alpha-32 P]-dCTP (250 μCi) and nylon membranes(Hybond N) are obtained from Amersham (Arlington Heights, Ill.).Colchicine (used as a control) is purchased from the Sigma ChemicalCompany (St. Louis, Mo.). Lipopolysaccharide (LPS) from Escherichia coliis purchased from DIFCO Laboratories (Detroit, Mich.). All plasticsupplies are purchased from VWR Scientific products (San Francisco,Calif.).

Northern Blotting

Total RNA is isolated by the guanidinium-cesium chloride method asdescribed before (N. S. Waleh, et al., 1994, Cancer Res., 54:838-843).Five to 10 μg of total RNA is electrophoresed in 1% agarose gelscontaining 6% formaldehyde. Following electrophoresis, gels are stainedwith ethidium bromide to visualize the positions of 28S and 18S RNA. TheRNA is then transferred to nylon membranes (Amersham Hybond N) bycapillary blotting and fixed to the filter by exposure to UV light. Theblots are probed with ³²P-labeled cDNA sequences of human TNF-alphaobtained from the American Type Culture Collection (ATCC). The TNF-alphacDNA is a 1.1 kb PstI fragment of plasmid pE4 in E. coli MM294 (ATCC39894). Hybridizations is carried out at 42° C. in 50% formamide, 5×SSC,5×Denhardt's solution, 0.1% SDS, and 0.3 mg/mL salmon sperm DNA. Filtersare washed by 1×SSC, 0.1% SDS, twice at room temperature for 15 min andonce at 55° C. in 0.1×SSC, 0.1% SDS for 1 hr. Filters are exposed toX-ray film at −70° C. using an intensifying screen (Coronex Hi-Plus).

Hybridized bands are quantified by analyzing the images obtained byusing a video densitometer (Applied Imaging Corporation, Santa Clara,Calif.). Film densities are calibrated using an optical-density wedge.

Treatment of PU5-1.8 murine macrophages with LPS (100 ng/mL) for 3 hresults in a significant increase (>7 fold) in the level of TNF-alphamRNA as determined by Northern blot analysis. Treatment of cells withcolchicine at 10 μM concentration has no effect on TNF-alpha mRNAexpression. However, addition of colchicine at 10 μM to the LPS treatedcultures resulted in substantial reduction of TNF-alpha mRNAaccumulation. The inhibition levels were 68% for colchicine.

To establish a concentration-effect relationship, macrophages areexposed to various concentrations of candidate tubulin inhibitors in thepresence of the stimulus LPS for 3 h. The amounts of TNF-alpha mRNAdeclines with increasing concentrations of the candidate tubulininhibitors. Thus, the above assay can be used to show that candidatetubulin inhibitors have the ability to reduce the level of TNF-alphaproduced by a cell.

Example 13 Cell Cycle Analysis with Flow Cytometry

The bromodeoxyuridine (BrdU) method for the analysis of the cell cyclecan be used for the study of cell kinetics. Bromodeoxyuridine is ananalogue of the DNA base thymidine and can compete with that base foruptake during the synthesis of DNA. So those cells that have beenactively synthesizing DNA during the time that BrdU is present can bepositive for it. It can be detected by a monoclonal antibody and bysimultaneously staining for DNA content with propidium iodide. Thepercentage of cells in G0/G1, S and G2/M can be determined. By alteringthe time that BrdU is present cell cycle times can also be assessed. Theprotocol used in this analysis is as follows. Cells are treated with 10μM BrdU for an appropriate time (30 mins). After harvesting and washingcells, the cells are fixed in ice-cold 70% ethanol while vortexing.Samples can stay in ethanol for up to 7 days. Sample is spun at 2000rpm, 5 min. Sample is washed twice in PBS. Cells are treated with 2Mhydrochloric acid for 20 min. at room temperature with frequent mixing.Acid is spun off (2000 rpm, 5 min.) and washed twice in PBS and once inPBS-T (PBS+0.5% Tween+0.05% w/v BSA). A 50 μl anti-BrdU antibody (SeraLab) is added, and left for 15 min. at room temperature. It is thenwashed twice in PBS-T. A 50 μl FITC-conjugated goat-anti-rabbitimmunoglobulins (DAKO) is added to it, and left for 15 min. at roomtemperature. It is then washed once in PBS-T. A 100 μl Ribonuclease, and400 μl propidium iodide (Stock is 50 μg/1 ml) is then added. Analyses isdone by flow cytometry (Fabbri F. et al. 2006, BMC Cell Biology, 7:6).

It is to be understood that the above descriptions are intended to beillustrative and not restrictive. Many embodiments will be apparent tothose of skill in the art upon reading the above descriptions. The scopeof the invention should, therefore, be determined not with reference tothe above descriptions, but should instead be determined with referenceto the appended claims, along with the full scope of equivalents towhich such claims are entitled. The disclosures of all articles andreferences, including patent applications and publications, areincorporated herein by reference for all purposes.

Example 14 Cell Cycle Analysis

HCT116 and Hela cells were obtained from ATCC. For DNA content analysis,2×10⁵ cells were washed twice with PBS and fixed in 70% ethanol. Cellswere treated with 100 units/mL RNase A for 20 minutes at 37° C.,resuspended in cold PBS containing Alexa Fluor® 405 fluorescent stain(Invitrogen) according to the manufacturer's protocol. Cells wereanalyzed by flow cytometry.

For DNA replication analysis, 2×10⁵ cells were incubated with 50 μmol/Lbromodeoxyuridine (BrdUrd) for 30 minutes. Cells were fixed in 70%ethanol and BrdUrd incorporation was determined by flow cytometricanalysis using an anti-BrdUrd-FITC antibody (Becton Dickinson, FranklinLakes, N.J.) according to the manufacturer's protocol. To assess thedegree of G2/M checkpoint, mitotic cells were detected by flow cytometryusing the mitosis-specific antibody GF-7. Fixed cells were incubated for30 minutes with GF7-phycoerythrin (PE) antibody (BD BiosciencesPharmingen), washed with PBS and analyzed by flow cytometry. FIG. 6compares the results obtained with DIPE and formula IIIB.

Example 15 Cell Cycle Analysis with Flow Cytometry

Programmed cell death (apoptosis) is an important homeostatic mechanismin the immune and other systems. The phenomenon of nucleardisintegration during apoptosis can be used as a marker to detect cellsundergoing this process. While a variety of methods are available todetect apoptotic cells the TUNEL assay allows the rapid phenotypicidentification of individual apoptotic cells using flow cytometry(FACS). Terminal transferase dUTP nick end labeling (TUNEL) is a commonmethod for detecting DNA fragmentation that results from apoptosis. Theassay based on the presence of nicks in the DNA that can be identifiedby terminal transferase, an enzyme that will catalyze the addition ofdUTPs that are secondarily labeled with a marker. It may also labelcells undergoing necrosis or cells that have suffered severe DNA damage.

Hela cells were obtained from ATCC. For DNA content analysis, 2×10⁵cells were washed twice with PBS and fixed in 70% ethanol. Cells weretreated with 100 units/mL RNase A for 20 minutes at 37° C., resuspendedin cold PBS containing Alexa Fluor® 405 fluorescent stain (Invitrogen)according to the manufacturer's protocol. Cells were analyzed by flowcytometry to characterize the cell cycle. To perform the TUNEL assay,cells were also fixed with 0.25% formaldehyde in the medium before theethanol treatment and then stained with the Apo-Direct® kit(eBioscience, San Diego, Calif.). The results of this assay for DIPE(control) and formula IIIB are shown in FIG. 7.

While preferred embodiments of the present invention have been shown anddescribed herein, it will be obvious to those skilled in the art thatsuch embodiments are provided by way of example only. Numerousvariations, changes, and substitutions will now occur to those skilledin the art without departing from the invention. It should be understoodthat various alternatives to the embodiments of the invention describedherein may be employed in practicing the invention. It is intended thatthe following claims define the scope of the invention and that methodsand structures within the scope of these claims and their equivalents becovered thereby.

1. A computer-assisted method of a designing of a tubulin inhibitorcomprising: a. determining an interaction between a tubulin protein anda chemical known to bind the tubulin protein by evaluating a binding ofthe tubulin protein to the chemical known to bind the tubulin protein;b. based on the interaction, designing a candidate tubulin inhibitor; c.determining an interaction between the tubulin protein and the candidatetubulin inhibitor by evaluating a binding of the tubulin protein to thecandidate tubulin inhibitor; and d. concluding that the candidatetubulin inhibitor inhibits the tubulin protein wherein the conclusion isbased on the interaction of step c).
 2. The method of claim 1, whereinthe tubulin protein is a three-dimensional structure comprising abinding domain of the tubulin protein.
 3. The method of claim 2, whereinthe binding domain of the tubulin protein is selected from the groupconsisting of colchicine binding domain, vinblastine binding domain, andpaclitaxel binding domain.
 4. The method of claim 3, wherein the bindingdomain of the tubulin protein is a colchicine binding domain.
 5. Themethod of claim 1, wherein the chemical known to bind the tubulinprotein is a three-dimensional structure.
 6. The method of claim 1,wherein the tubulin protein is derived from a crystal of the tubulinprotein.
 7. The method of claim 1, wherein the designing is performed inconjunction with a computer modeling.
 8. The method of claim 2, whereinthe binding domain of the tubulin protein is an intradimer surface. 9.The method of claim 2, wherein the binding domain of the tubulin proteinis an interdimer surface.
 10. The method of claim 2, wherein the bindingdomain of the tubulin protein is a surface facing inside of amicrotubule near an interprotofilament interface at a distance from anylongitudinal interface.
 11. The method of claim 10, wherein the surfaceis a paclitaxel binding site.
 12. The method of claim 1, wherein thedesigning involves replacing a substituent on the chemical known to bindthe tubulin protein with another substituent wherein the othersubstituent improves the binding of the candidate tubulin inhibitor withthe tubulin protein.
 13. The method of claim 1, wherein the interactionis steric interaction, van der Waals interaction, electrostaticinteraction, solvation interaction, charge interaction, covalent bondinginteraction, non-covalent bonding interaction, entropically favorableinteraction, enthalpically favorable interaction, or a combinationthereof.
 14. The method of claim 1, wherein the candidate tubulininhibitor is an analogue of the chemical known to bind the tubulinprotein.
 15. The method of claim 1, wherein the chemical known to bindthe tubulin protein is a ketone that is a thyroxine analogue.
 16. Themethod of claim 1, further comprising a step of chemically synthesizingthe candidate tubulin inhibitor.
 17. The method of claim 16, furthercomprising evaluating a tubulin inhibitory activity of the candidatetubulin inhibitor and selecting the candidate tubulin inhibitor based onthe evaluation.
 18. The method of claim 17, wherein the evaluating thetubulin inhibiting activity involves an assay technique.
 19. The methodof claim 1, wherein the candidate tubulin inhibitor is a compound offormula I, its pharmaceutically acceptable salts, or prodrugs thereof:

wherein: R₁ and R₅ are halogens; R₂, R₃, and R₄ are independentlyselected from the group consisting of hydrogen, hydroxyl, halogen,ester, optionally substituted alkoxy, optionally substituted amine,phosphate, optionally substituted alkyl, and optionally substitutedacetyl; and R₆, R₇, R₈, R₉, and R₁₀ are independently selected from thegroup consisting of hydrogen, hydroxyl, halogen, optionally substitutedalkoxy, optionally substituted amine, phosphate, optionally substitutedalkyl, optionally substituted alkenyl, optionally substituted alkynyl,nitroso, carboxyl, optionally substituted cycloalkyl, and optionallysubstituted heterocyclic.
 20. The method of claim 19, wherein thecandidate tubulin inhibitor is a compound of formula II or itspharmaceutically acceptable salts or prodrugs:

wherein: R, R′, R₂, R₄, R₆, R₇, R₉, and R₁₀ are independently selectedfrom the group consisting of hydrogen, hydroxyl, halogen, optionallysubstituted alkoxy, optionally substituted amine, phosphate, optionallysubstituted alkyl, and optionally substituted acetyl.
 21. The method ofclaim 20, wherein the candidate tubulin inhibitor is a compound offormula III or its pharmaceutically acceptable salts or prodrugs:

wherein: R, R₇, R₉, and R₁₀ are independently selected from the groupconsisting of hydrogen, hydroxyl, optionally substituted amine,phosphate, and optionally substituted alkyl.
 22. The method of claim 21,wherein the candidate tubulin inhibitor is a compound of formula IIIA orits pharmaceutically acceptable salts or prodrugs:


23. The method of claim 21, wherein the candidate tubulin inhibitor is acompound of formula IIIB or its pharmaceutically acceptable salts orprodrugs:


24. The method of claim 21, wherein the candidate tubulin inhibitor is acompound of formula IIIC or its pharmaceutically acceptable salts orprodrugs:


25. The method of claim 21, wherein the candidate tubulin inhibitor is acompound of formula IIID or its pharmaceutically acceptable salts orprodrugs:


26. The method of claim 21, wherein the optionally substituted alkyl issubstituted with an optionally substituted heterocyclic.
 27. The methodof claim 26, wherein the optionally substituted heterocyclic is selectedfrom a group consisting of azeridine, azetidine, pyrrole,dihydropyrrole, pyrrolidene, pyrazole, pyrazoline, pyrazolidine,imidazole, benzimidazole, triazole, tetrazole, oxazole, isoxazole,benzoxazole, oxadiazole, oxazoline, oxazolidine, thiazole, isothiazole,pyridine, dihydropyridine, tetrahydropyridine, quinazoline, pyrazine,pyrimidine, pyridazine, quinoline, isoquinoline, triazine, tetrazine,and piperazine.
 28. The method of claim 27, wherein the candidatetubulin inhibitor is a compound of formula IIIE or its pharmaceuticallyacceptable salts or prodrugs:


29. A computer system containing a set of information to perform adesign of a tubulin inhibitor having a user interface comprising adisplay unit, the set of information comprising: a. logic for inputtingan information regarding a binding of a tubulin protein to a chemicalknown to bind tubulin protein; b. logic for designing a candidatetubulin inhibitor based on the binding of the tubulin protein to thechemical known to bind tubulin protein; c. logic for determining aninformation regarding a binding of the tubulin protein to the candidatetubulin inhibitor; and d. logic for making a conclusion regarding atubulin inhibitory properties of the candidate tubulin inhibitor basedon the determination of step c).
 30. A computer-readable storage mediumcontaining a set of information for a general purpose computer having auser interface comprising, a display unit, the set of informationcomprising: a. logic for inputting an information regarding a binding ofa tubulin protein to a chemical known to bind tubulin protein; b. logicfor designing a candidate tubulin inhibitor based on the binding of thetubulin protein to the chemical known to bind tubulin protein; c. logicfor determining an information regarding a binding of the tubulinprotein to the candidate tubulin inhibitor; and d. logic for making aconclusion regarding a tubulin inhibitory properties of the candidatetubulin inhibitor based on the determination of step c).
 31. The systemof claim 29, wherein the chemical is a ketone which is a thyroxineanalogue.
 32. The computer readable media of claim 30, wherein thechemical is a ketone which is a thyroxine analogue.
 33. An electronicsignal or carrier wave that is propagated over the internet betweencomputers comprising a set of information for a general purpose computerhaving a user interface comprising a display unit, the set ofinformation comprising a computer-readable storage medium containing aset of information for a general purpose computer having a userinterface comprising a display unit, the set of information comprising:a. logic for inputting an information regarding a binding of a tubulinprotein to a chemical known to bind tubulin protein; b. logic fordesigning a candidate tubulin inhibitor based on the binding of thetubulin protein to the chemical known to bind tubulin protein; c. logicfor determining an information regarding a binding of the tubulinprotein to the candidate tubulin inhibitor; and d. logic for making aconclusion regarding a tubulin inhibitory properties of the candidatetubulin inhibitor based on the determination of step c).
 34. A method oftreating a disease comprising administering to a patient in need thereofan effective amount of at least one compound of formula I, itspharmaceutically acceptable salts, or prodrugs thereof:

wherein: R₁ and R₅ are halogens; R₂, R₃, and R₄ are independentlyselected from the group consisting of hydrogen, hydroxyl, halogen,ester, optionally substituted alkoxy, optionally substituted amine,phosphate, optionally substituted alkyl, and optionally substitutedacetyl; and R₆, R₇, R₈, R₉, and R₁₀ are independently selected from thegroup consisting of hydrogen, hydroxyl, halogen, optionally substitutedalkoxy, optionally substituted amine, phosphate, optionally substitutedalkyl, optionally substituted alkenyl, optionally substituted alkynyl,nitroso, carboxyl, optionally substituted cycloalkyl, and optionallysubstituted heterocyclic.
 35. The method of claim 34, wherein thecompound is of formula II or its pharmaceutically acceptable salts orprodrugs:

wherein: R, R′, R₂, R₄, R₆, R₇, R₉, and R₁₀ are independently selectedfrom the group consisting of hydrogen, hydroxyl, halogen, optionallysubstituted alkoxy, optionally substituted amine, phosphate, optionallysubstituted alkyl, and optionally substituted acetyl.
 36. The method ofclaim 35, wherein the compound is of formula III or its pharmaceuticallyacceptable salts or prodrugs:

wherein: R₆, R₇, R₉, and R₁₀ are independently selected from the groupconsisting of hydrogen, hydroxyl, optionally substituted amine,phosphate, and optionally substituted alkyl.
 37. The method of claim 35,wherein the compound is of formula IIIA or its pharmaceuticallyacceptable salts or prodrugs:


38. The method of claim 35, wherein the compound is of formula IIIB orits pharmaceutically acceptable salts or prodrugs:


39. The method of claim 35, wherein the compound is of formula IIIC orits pharmaceutically acceptable salts or prodrugs:


40. The method of claim 35, wherein the compound is of formula IIID orits pharmaceutically acceptable salts or prodrugs:


41. The method of claim 36, wherein the optionally substituted alkyl issubstituted with an optionally substituted heterocyclic.
 42. The methodof claim 41, wherein the optionally substituted heterocyclic is selectedfrom a group consisting of azeridine, azetidine, pyrrole,dihydropyrrole, pyrrolidene, pyrazole, pyrazoline, pyrazolidine,imidazole, benzimidazole, triazole, tetrazole, oxazole, isoxazole,benzoxazole, oxadiazole, oxazoline, oxazolidine, thiazole, isothiazole,pyridine, dihydropyridine, tetrahydropyridine, quinazoline, pyrazine,pyrimidine, pyridazine, quinoline, isoquinoline, triazine, tetrazine,and piperazine.
 43. The method of claim 42, wherein the candidatetubulin inhibitor is a compound of formula IIIE or its pharmaceuticallyacceptable salts or prodrugs:


44. The method of claim 34, wherein the treating comprises inhibitingtubulin protein function.
 45. The method of claim 34, wherein thedisease is selected from the group consisting of cancer, inflammation,metabolic disease, gout, CVS disease, CNS disease, disorder of thehematolymphoid system, disorder of endocrine and neuroendocrine,disorder of urinary tract, disorder of respiratory system, disorder offemale genital system, and disorder of male genital system.
 46. Aprocess of manufacturing a compound of formula IIIB or itspharmaceutically acceptable salts or prodrugs:

comprising: (a) nitrating1-(3,5-diiodo-4-(4-methoxyphenoxy)phenyl)ethanone to form as anintermediate 1-(3,5-diiodo-4-(4-methoxy-3-nitrophenoxy)phenyl)ethanone;and (b) reducing the intermediate of step (a) to form the compound offormula IIIB.
 47. The process of claim 46, wherein the nitrating iscarried out in the presence of nitric acid and concentrated sulfuricacid in an organic solvent.
 48. The process of claim 47, wherein theorganic solvent is methylene chloride.
 49. The process of claim 46,wherein the reducing is carried out in the presence of tin(II) chloride.50. A process of manufacturing a compound of formula IIIA or itspharmaceutically acceptable salts or prodrugs:

comprising: (a) reacting a compound of formula IIIB:

with a metal nitrate in the presence of a strong acid to form adiazonium intermediate; and (b) refluxing the diazonium intermediate inthe presence of a strong acid to form the compound of formula IIIA. 51.The process of claim 50, wherein the metal nitrate is sodium nitrate.52. The process of claim 50, wherein the strong acid of step (a) issulfuric acid.
 53. The process of claim 50, wherein the strong acid ofstep (b) is sulfuric acid.
 54. The process of claim 50, wherein thestrong acid of step (a) and step (b) is sulfuric acid.